The ones I've run in to are custom game modes, menu screens, no coding on the select screen. Number limit on variables, no saving, no online, limit on special effects on screen, Some hard coded fighting game mechanics, limited stage coding options.
You can't check the order of the characters you will face in the future on a random enemy setting. It causes trouble for UMK3 ladder.
Can't use more than one sprite file per character = problems with high color sprites and alternate costumes.
no 3D effects
There are workarounds for some of these things, but you have to be clever to find ways of doing something that wasn't meant to be. You don't have total freedom.