|Replacing the model format with one which allows external animations. Something similar to the Unreal Tournament games.|
I couldn't agree more and I know which model format it should be, Doom3's md5. Xreal, which like ioquake3 evolved from quake3, has implemented this so it's entirely possible that it could be ported to ioquake3.
Not only would it be good to use md5 for the models, it wouldn't hurt to use it for the player characters too.