As you said, those two games are from Ubisoft and as such one can only guarantee that what you have is an unfinished/unoptimized and poorly coded Console port of a game.
Have you tried playing any other non-Ubi game? this will tell you whether is your pc, your gamepad drivers
conflicting with the games or the ubi games.
Also, perhaps going to the UBI forums yield better results? I am betting you will not be the only one with those issues. Why would you want to play with a gamepad and not a mouse is not really the question here, although, I am curious, hence, why I ask
but again, if you visit those forums, I am sure, others have the issue and a possible answer.
I would start by updating all my drivers and checking to see if that solves the issue, but I strongly believe the easiest of the test is to play a different game first.