This is in no way your fault Eli. Actually, in terms of professional game making, they are expecting a lot out of your game in a meager 3 minutes.
That girl chose a really ambitious project, and a very risky one at that. Graphics and music wise, it just looked a lot more appealing. The main problem I saw with her entry was that the players were not interacting with the game. Clicking a button 2000 times, regardless of the effects or story displayed, is going to get boring after a while. In case, I agree with the judges decision for not letting her move forward. The game is just a graphic novel, and you can get that just by buying a book.
Even though I think the presentation of your game did not give it justice, I can see why it was considered fun. You get right into the action immediately, and the game is simple and easy enough to pick up. The fear is that is just looks a bit generic, and the game play mechanic is something not tried too often. The games that did try it were not ground-breaking… so it might be an uphill climb.
Of course, it is as you said, all these things can be addressed through polish. 2 minutes is really a deal breaker for RPG’s and text based adventure games which need more time to get to the meaty parts. But, the name of the show is “The next game boss”, not “The next graphical presentation addict”. Seriously, I think the way they are doing it so far is really forcing you guys to think about the game aspect more than anything else.