There can be some pretty cool compositing and texture done by combining things.
I had an issue a few yeays ago, when the winner had cut to full frame video for a large chunk of the entry, since the rules state- 30 SECONDS OF STUDENT ANIMATION. It also used to say (I didn't check for it this year) that you can include video and such in your entry. The only way I know to combine the two rules and still be complients is how we did it the last couple years-
www.shsrobotics.org (Check out the MEDIA- VIDEO- ANIMATION section) Out team has shown how you can include both.
If you can do 2D and include it in a 3D environment, then go for it. One of my clients just paid many tens of thousands of dollars (to anonther vendor) to achieve that exact effect. (Live video- 2D - and 3D) So its very good skills to learn and adds a unique look and feel to the video.