So, with the movesets, I'm not entirely sure, as I only attempted replacing all movesets with vBrawl movesets for 3.2 (Without touching the .rels), and Pikachu's Up+B was the only thing that didn't work right, but I haven't a clue for PM 3.6
With skins, Project M uses vBrawl bonesets, so you can place any (compatible) skin over a character (Including Lucario skins over Mewtwo and/or Marth skins over Roy; dunno about the other additional PM characters tho, since I never played past 3.5); I dunno about 3.6, tho, but with 3.5, there is a single bug with skins, where replacing Mario/Dr. Mario costumes, while any can technically work, if it's not a PM skin, it'll have the wrong texture on his Side+B
Well I already started with some stages and some skins for dr mario
, mario, lucario, luigi and fox but I do not think they become a problem because before I had already tried several skins from dr mario and they worked very well the intersante will be with the stages
so far I have only replaced one which was delfino plaza for its version of wii u
soon we will see what happens ...
thanks for answering