In general I can adapt to mostly anything (except playing Soul Calibur with a stick, I just can't do it...)
I too am not a big fan about up being used for jumping. I feel it should be reserved for fighter games where it actually makes more sense.
WASD + Mouse for aiming in a sidescroller is something I'm not a too big fan of as well. I find it better to aim like in Contra, where you aim with the movement buttons, than aiming with the mouse. Mostly because in almost every wasd sidescroller, it doesn't seem necessary. Most of the time it feels like the dev actually wanted to make an fps, but couldn't, so he just made it 2D and kept the layout.
As a thought experiment, take one such game and think about how it works, then replace the mouse aiming with Contra style aiming. The game should work just as well, probably better for some. I currently can't think of a game mechanic that requires mouse aiming.