OK. Let me quote a few passages from Wikipedia's rules. Read them and see if my points here make sense.

On the point of the acceptability of the sources used, since the sources are the original pieces of fiction--which expressly mention the information being listed--this information is coming from a primary source:

Primary sources are sources very close to the origin of a particular topic. An eyewitness account
of a traffic accident is an example of a primary source. Other examples include archeological
artifacts; photographs; historical documents such as diaries, census results, video or transcripts
of surveillance, public hearings, trials, or interviews; tabulated results of surveys or
questionnaires; written or recorded notes of laboratory and field research, experiments or
observations, published experimental results by the person(s) actually involved in the research;
autobiographies, original philosophical works, religious scripture, administrative documents, and
artistic and fictional works such as poems, scripts, screenplays, novels, motion pictures,
videos, and television programs.

The argument that Wikipedia is not a reliable resource is therefore moot, since each listing includes the name of the work in which the character is asserted to have attended the university in question, and such claims are made plainly--as a point of fact--in the material, so that no interpretation or analysis of the material is needed to reach that conclusion.

On the point of whether the article constitutes original research:

Primary sources that have been published by a reliable source may be used in Wikipedia, but only with
care, because it is easy to misuse them. For that reason, anyone—without specialist knowledge—who
reads the primary source should be able to verify that the Wikipedia passage agrees with the primary
source.
Any interpretation of primary source material requires a reliable secondary source for that
interpretation. To the extent that part of an article relies on a primary source, it should:
* only make descriptive claims about the information found in the primary source, the accuracy and
  applicability of which is easily verifiable by any reasonable, educated person without specialist
  knowledge, and
* make no analytic, synthetic, interpretive, explanatory, or evaluative claims about the information
  found in the primary source.

As this information is a direct compilation of "descriptive claims about the information found in the primary source," and as "the accuracy and applicability [of this material] is easily verifiable by any reasonable, educated person" reading or watching the material, and since each piece of information is not the subject of any analysis or synthesis of new conclusions or information (which is the kind of synthesis that is to be avoided) then the collection of this material does not violate the strictures on original research. To continue and provide some context for the quote used by Rejectwater:

Material published by reliable sources can inadvertently be put together in a way that constitutes
original research. Synthesizing material occurs when an editor comes to a conclusion by putting
together different sources. If the sources cited do not explicitly reach the same conclusion, or if
the sources cited are not directly related to the subject of the article, then the editor is engaged
in original research. Summarizing source material without changing its meaning is not synthesis; it
is good editing. Best practice is to write Wikipedia articles by taking claims made by different
reliable sources about a subject and putting those claims in our own words on an article page, with
each claim attributable to a source that makes that claim explicitly.

Editors should not make the mistake of thinking that if A is published by a reliable source, and B
is published by a reliable source, then A and B can be joined together in an article to come to the
conclusion C. This would be synthesis of published material which advances a position, which
constitutes original research.[6] "A and B, therefore C" is acceptable only if a reliable source has
published this argument in relation to the topic of the article.

Since the information listed in this article does not try to reach any conclusion, but rather to compile facts in evidence to anyone reading/watching the original material, no synthesis is occurring. The A+B=C argument only applies if new information is concluded by the combination of A and B. That does not occur here. There has been a logical error in the assertion that it has. The claim is that "You take Tony Stark who went to MIT (A), then you take Chuck who went to Stanford (B), and you realize that there are any number of fictional characters whose back story includes attending a real university (C)." This is not a conclusion reached by the article. At no point does the chain of logic state:

The fact that there are characters in fiction who are claimed to have attended real universities is a fact. That is not a conclusion. The article is not trying to assert the truth or falsehood of this fact, but simply to compile the information that is available without analysis to that effect. Inclusions that would violate the rule you cite would be those where it is only implied that the character went to a given school, but that several clues would have to be analyzed to support that conclusion. That is not the kind of material this article has been created to present. To expand on this point (from Wikipedia:These are not original research):

Compiling related facts and information from independent sources is part of writing an encyclopedia.
For example, multiple secondary sources are usually required before the notability of a subject is
established. Those sources must then be combined to produce a cohesive, comprehensive, and coherent
article. Neutral point of view requires presenting all significant viewpoints on an issue, and may
include collecting opinions from multiple, possibly biased and/or conflicting, sources. 'Organizing
published facts and opinions — without introducing your opinion or fabricating new facts, or
presenting an unpublished conclusion — is not original research.'

On the point of whether this list is appropriate for Wikipedia, or is non-encyclopedic:

Lists have three main purposes:

Information
The list may be a valuable information source. This is particularly the case for a structured list.
Examples would include lists organized chronologically, grouped by theme, or annotated lists.

Navigation
Lists contain internally linked terms and thus in aggregate serve as natural tables of contents and
indexes of Wikipedia. If users have some general idea of what they are looking for but do not know
the specific terminology, they could browse the lists of basic topics and more comprehensive lists
of topics, which in turn lead to most if not all of Wikipedia's lists, which in turn lead to related
articles. Users without a specific research goal in mind might also find the articles listed in
articles' see also sections useful. Lists are also provided in portals to assist in navigating their
subjects, and lists are often placed in articles via the use of series boxes and other navigational
templates.

Users with a specific research goal, described by one or two words that they can spell correctly,
are likely to find Wikipedia's search box useful.

Development
Some lists are useful for Wikipedia development purposes. The lists of related topics give an
indication of the state of Wikipedia, the articles that have been written, and the articles that
have yet to be written. However, as Wikipedia is optimized for readers over editors, any lists
which exist primarily for development or maintenance purposes (such as a list of red link articles
needed) should be in project or user space not the main space, if the list is not otherwise
encyclopedic.

Since this list both allows the user to easily navigate an alphabetical list of characters which then leads to articles about the character, the source, the author, and the university in question, it both ties information together (without drawing conclusions) and allows users to more effectively navigate Wikipedia even if they are unsure of what they are looking for (e.g., "I know that one of the characters in book x went to an Ivy League college, but I can't remember which. How can I find that information on Wikipedia?"). This actually fulfills two different purposes for valid lists by being both informational in and of itself, by collecting information about which characters went to which schools, and by being navigational, by helping the user navigate articles on related information.

On the topic of whether or not this article falls under "Wikipedia is not a directory", here are the relevant quotes for context:

Wikipedia is not a directory of everything that exists or has existed.[3] Wikipedia articles are not:

1. Lists or repositories of loosely associated topics such as (but not limited to) quotations,
aphorisms, or persons (real or fictional). If you want to enter lists of quotations, put them into
our sister project Wikiquote. Of course, there is nothing wrong with having lists if their entries
are famous because they are associated with or significantly contributed to the list topic, for
example Nixon's Enemies List. Wikipedia also includes reference tables and tabular information for
quick reference. Merged groups of small articles based on a core topic are certainly permitted. (See
Lists (stand alone lists) - appropriate topics for clarification.)
.
.
.
5. Non-encyclopedic cross-categorizations, such as "People from ethnic/cultural/religious group X
employed by organization Y" or "Restaurants specializing in food type X in city Y". Cross-categories
like these are not considered sufficient basis to create an article, unless the intersection of those
categories is in some way a culturally significant phenomenon. See also Wikipedia:Overcategorization
for this issue in categories.

To address the first point, this is not simply a list of loosely related fictional characters, it is an encyclopedic cross-categorization. It does not just list all fictional characters that went to college, but provides a framework for crossing from one piece of information to another.

To address the second point, the following section from Wikipedia:Overcategorization helps to clarify:

Non-defining or trivial characteristic
  Example: Bald People, Famous redheads
In general, categorize by what may be considered notable in a person's life, such as his or her
career, origin and major accomplishments. In contrast, someone's tastes in food, their favorite
holiday destination, or the number of tattoos they have may be considered trivial. Such things may be
interesting information for an article, but not useful for categorization. If something could be
easily left out of a biography, it is likely not a defining characteristic.

Note that this also includes grouping people by trivial circumstances of their deaths, such as
categorizing people by the age at which they died or by whether they still had unreleased or
unpublished work at the time of their death. Even though such categories may be interesting to some
people, they aren't particularly encyclopedic. 

It seems reasonable that the university a character attended may be considered a "major accomplishment" as long as the character graduated, or if gaining acceptance to said university in itself would be considered a notable accomplishment (for instance Chuck attending Stanford). According to this elaboration, the intersection of character and university would be valid as it is based on "what may be considered notable in a person's life."

In addition, the following statement from Wikipedia:Overcategorization#Award_recipients makes a fairly strong argument as to why this material should be a list rather than a categorization:

Award recipients
People can and do receive awards and/or honors throughout their lives. In general (though there are a
few exceptions to this), recipients of an award should be grouped in a list rather than a category.

The university one graduates from (or in cases of very exclusive schools the university one is admitted to) is tantamount to an award. In point of fact, graduation provides a degree which is an award. That would then be a solid reason to prevent this list from being re-invented as a category, since according to this passage, it is plain that it should be a list.


Lists of people

Several articles contain or stand alone as lists of people - for instance, usually an article on a
college includes or links to a list of notable alumni. Such lists are not intended to contain
everyone (e.g. not all people who ever graduated from the school). Instead, inclusion on the list
should be determined by the criteria above. Because of this, "notable" is assumed, and that word (or
similar, such as "famous," "noted," "prominent," etc.) should not be included in the title of the
list article. See list naming conventions.

Editors who would like to add themselves to such lists should instead use categories of editors for
this purpose, e.g. Category:Wikipedians by alma mater.