This reply might be a little late for this year's app deadline (and I've answered this a couple of times before on other threads), but for posterity:
They're looking to identify good people that are good writers-- that's it. They're not necessarily worried about your ability to finish a feature script because they'll make sure you finish one in the program (at least three, actually). I'd submit only the work you're most proud of. In terms of # of pages, that always varies from applicant to applicant, but people that have been doing this for a while can identify whether or not you're a good writer much, much sooner than page 200.
I ended up sending two half-hour pilots and the first 10 pages of a feature script that I'd only planned on writing the rest of (never touched it again). Unless you just have 200 amazing pages, I'd think of the large stack of applications these professors (who are also teaching classes and writing for their own careers) have on their desks. It sounds like you've already identified your best work, so I wouldn't worry that it's less than 100 pages. If you do have a killer opening to one of those features, definitely wouldn't hurt to include 10-15 pages of it, but if you know you can do better, I'd leave it out.
In the first quarter, all first-years have to take an introductory course called 431 where you essentially outline an entire feature (or pilot) but only write the first act. You're actually not even allowed to take a 434 (the full feature-length script course, and the one you'll take most often as a Screenwriting MFA) or an original pilot class until your second quarter anyway. Your personal statement (and subsequent interview, if invited) is probably the best place to demonstrate your persistence and dedication as a writer. So, to put it in conversational terms...
Most of your application should say: "This is what I could bring to your program in terms of character, personality, and professionalism."
The pages you send should simply say: "And, oh by the way, I'm a great writer, too."
Hope that helps-- good luck with your applications!