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I'm having some issues playing at least the first game with controllers, and I'd like to know if it's because I'm on Linux/Wine/x360ce or if they are bugs in the game.

The more serious one is that sometimes one player just gets cut off with the controller ceasing to control, and this can't be recovered. I found references to this one on the web, and it seems to be a bug in the game. It can be reproduced in the Leaky Cauldron by choosing the pinboard and exiting without making a selection. I hope it doesn't happen in many other places :(

The other one is not very bad now that I figured out what was going on, but before that it was causing me a lot of headache; the game just seems to entirely disregard my controllers until it has seen enough axis movement from them. I now give the thumbsticks a twirl and press the triggers during the intro movie, and after that it works fine. The second player also needs to do this before joining game. This might be because of my setup, but not entirely sure.
i have no problems in windows. the problems is therefore likely a linux based issue.