Biggest problem I had going from mouse to tablet was from 1ms polling rate to whatever the tablet is. Seems like it wouldn't be a big problem...nope. I was completely unable to do fast slider jumps like in the map
The Pretender and would just fail on them whenever they popped up. Took me several months to get used to that.
As for my biggest con with the mouse, I would have to reposition the mouse a lot because it would drift somewhere weird when playing maps that moved in large circles as the map went on.
Lily - Chloe was a particularly bad offender of this.
Not sure if this was quite what you were asking but yeah, those were the biggest gameplay changing characteristics I have with both.