I am a character animation BFA, currently taking a class in experimental animation, and I am a little torn between the two departments as well. I don't know everything about the department, but I'll try to do the best I can to illustrate both with you.  

I think the overall difference between the two is the main goal of what you are doing there, at least from what I've seen.  Maybwe I'll get an angry mob coming at me for saying this, but I think the purpose of the character department is to get a job at a studio, and the purpose of the experimental department is to make art.  Not saying that studios do not make art, or that character students do not make art.  and that's not saying that experimental students do not get jobs.  It's just that the emphasis is a a little split, it feels like.

The character animation department really only works with traditional hand-drawn animation, and CG animation.  But they give a technical foundation for that thing.  For example: Last semester BFA 1 character animation students were told to do a walk cycle.  The teacher showed us how walks work in motion, what foor goes where and how many frames a casual walk would take, how to break down the keys, etc.  From that foundation the next assignment was to do a walk with personality where we took that technical information and played around with it.  when the BFA 1's in the experimental department were given the assignment to do a walk cycle, they were not told any of those technical things.  Their teacher simply told them to make one and come back to class.  Many of them seemed dissapointed with the lack of structure in the class.  Which you may like or may not, but I'm giving you this information to make your own opinion.

another difference is that character's class schedule is very rigid.  In character you have little to no free time to do things outside of your class assigments.  You can do it, but you have to be good at time management.  In experimental, at least from how it's been told to me, there's more time to choose what you want to do with your time, take outside classes, and focus on your own art making.

Character focuses on what the industry wants, and what will get you a job and where.  Experimental is about making the art you want to make, whether it's marketable or not.  

You can take experimental classes while in character.  I persoanlly want to be a puppet fabricator for stop motion. We have no classes on that in character animation, but I am taking a stop motion class currently, and plan on taking more in the future.   Character animation students have been successful working with "experimental" mediums in their end of the year films and other projects before.  Last year, a partialy stop motion animated film got into the producer's show.

Really, it comes down to you, and what your focus is, and what you feel your college experience should be about.  Sometimes I wish I had gone into experimental animation instead, so it would leave me more time to work practice puppet building and take more classes dealing with it early on, but I think overall I'm glad that I'm in character, and I value the structure.