There aren't many games out there that allow you to change controls in-game; only ones I can think of at the top of my head are the original, KTG, Boshy, and K3, and the only one of those I'd recommend are KTG. There are key-binding programs out there that I'd recommend using, specifically AutoHotkey.
I don't know what to recommend exactly, so I guess just check out all of Ef's games (Colorless Sorrow 1+2, destroy the venus, destroy the mercury, destroy the pluto, Phantom Needle 1+2 (if you can find them)); they're all needle, but really good needle, and they shouldn't be resource-intensive at all.