Need advice on type of surroundings to visit.

So, next year I'll be heading to Japan via my college's study abroad program. What do you all think about what kind of city I should live in? They have 5 colleges/universities you can attend, in varying sizes. As a gaijin, would it be fun to go to a smaller city, or maybe stick with somewhere safer like Kyoto? What kind of pros/cons come from small and large cities?

It really depends on you and the type of person you are. Are you a city guy? Then Tokyo and/or Osaka might be for you. Each city/area has it's own charm, it's just a matter of finding one that fits with your style.
That being said, Nagoya rocks! Not too big, not too small. Also Kyoto is cute and charming, but not too crazy.

Nagoya

I've been in Aichi for 4 years and I certainly cannot say that Nagoya rocks.Actually, some foreigners have compared it with the cities they are living and say that people from Nagoya are exceptionally negative towards foreigners.As a matter of fact, last week one old lady hit me in front of many people because I came too close to her in the croud ( I was trying to get in better position for a photo of the annual parade), and noone tried to stop her.
My advice is Hiroshima or Kyoto, or Sendai,thogh Sendai is cold.
Yes, and it will be extremely difficult for you to find an appartment in Nagoya-many landlords refuse to foreigners.In Osaka it was easier to find an appartment.
People from Hiroshima and Kyoto are kind and helpful, there are many places to go, and Hiroshima is cheaper.