wow, all of this is very interesting and important stuff to know if you're looking to release a game commercially using fusion.. I'm also looking to release on steam and gamepad support is a must.. this will cause all kinds of problems unless a solution is found. It can be really hard to bounce back from bad reviews on steam so this will make it very hard to succeed on what is the most important market for indie games.
I really wish clickteam would chime in on this.. The 2.5+ update seemed to be focused on the more demanding developers, functional gamepad support on steam would be great as part of that package IMHO.