Hey. I can help out with that. First...

1. One Crew, unless you give every crew someone who can use rapid transportation. Running more than one crew doesn't work in such a closed world like One Piece. If this was say, Naruto, Bleach, or the like where rapid transport is a thing and/or the world is the size of japan instead of say, the size of the WORLD, you can have different factions.

2. A Heroes Journey might be the best storytyping to keep everyone together. If people wanna be the temporary bad guy, you can let them no prob, but the main chars should just be the 'straw hats', if that makes sense while you handle the arcs and stuff, with other players maybe making villains if they so wish.

3. DO NOT be anal about powersets or characters. The less restrictive you are on stuff that aren't outright broken, the better things will be. Lots of RPs died after starting due to being too restrictive on character design.