Ever since the awake patch, I've noticed there were several issues when playing with a controller/joystick. I am currently alternating between Logitech f310 and logitech f710 and have been using these controllers since 2013. There have always been direct support for these controllers; did not have to use steam controls nor have to launch maplestory via steam. (They were plug and play controllers, no additional configuring outside of the in game controller settings required.)
My characters are based in Scania and have discovered different issues on several characters:
1) Kanna's shikigami haunting only triggers the first hit when using the controller (does not follow up with hit 2 or 3 even when holding or mashing button), but works fine with the keyboard. Note that this was not an issue prior to the awake patch.
2) Demon slayers have the same issue with kanna that the demon arch lash only triggers the first hit on controller, does not follow up with hits 2-3-4. No issues with keyboard.
3) Demon slayers are not able to jump/glide using a controller
4) Thunderbreakers are not able to perform high vertical jump using controller's Jump and up, and are not able to perform combos properly when playing with such controllers.
These are some examples that i am aware of, based on the characters that i have played since the awake update. There might also be similar bugs that i'm unaware of (controller related issues)