I made the changes because I feel that the stages I removed were very unfair (Luigi's Mansion - camping, got rid of a lot of stages that DDD can easily 0-death on, etc). Other stages that I deem unfair would also include Port Town Aero Drive, Onett (Insanely easy wall infinites here), and others.
I only DDD banned 2 stages, Castle Siege and Green Greens. It's so easy to get a wall infinite on Green Greens it's not funny (but it's a good counterpick for some characters that aren't DDD) and its very possible to chaingrab them off the screen on Siege. Pictochat, PS1, Delfino and RC are not DDD banned because it is more difficult to get the wall infinite/off-screen chaingrab.
If you have a problem with a stage, just ban it. But remember to use your ban wisely.