I'd have to check better, but I guess the only stage changes from 2.6 to 2.6b were SSE Jungle, which has a symmetric set of platforms now, and Norfair, which has a different set of entry points, item spawns and stuff. Oh, and Final Destination, which has another collision edit that fixes some issue with the previous one.
I also made a small change to the lighting of Battlefield, but that one doesn't change the way it works at all. And some fixes to Skyloft, but nothing that drops compatibility.
From 2.5b to 2.6, the Starfox one has no tilts, WarioWare had a wind removal... I don't know if there's anything else, I'll check it in case you think there may be something else.