Little in my view. I had no issue with the controls, they were simply different and you either got them or you didn't, like any other game.
I felt the main issues were with the SP Campaign, specifically I felt:
1 - it was a little too short, not so much in terms of missions, but in terms of where they took you - i.e. the story converyed felt a little rushed and incomplete
2 - it veered a little too much in tone, from a more somber, gritter combat tone to the usual hunks exchanging tough talk stuff. Personally, with so much of the latter I'd have preferred it to be more consistently focused on the former
3 - the writing was variable as was the focus on character development
The MP I really like and I felt they got it just right. I also think KZ2 received too little praise for actually having 'bots and decent ones at that.