Those are my fears as well, but with a few years left in the show, I would assume any issues with House's gift will be resolved. As for the Wilson and Cuddy conundrum, I do not think Wilson will lose his place as #1 best friend/confidant/conscience/support. Whatever happens with Cuddy, I do not think will change that, even if their relationship went on further than any sexual encounter. He was still #1 with Stacy around, I would imagine, even if we don't have canon evidence.