A hypothetical addition to a hypothetical WipEout game will certainly be crappy. That's your reason for not wanting a skin editor?
If they do it right, it can be as good as Armored Core's system, and Armored Core's customization is far from crappy (Which we could say was about the level of the Pulse online editor sans Photoshop.)
Will it be hard for SL to implement such a system: yes, definitely. Is it possible in WipEout HD? I don't think so myself, but I think it's something they should seriously consider for the next WipEout game. It adds personality to the ships, each player has his personal colours. I find that pretty fun... Think about it, clans, groups of friends, WipEoutZone could have their very own skin. Wouldn't the WipEout HD World Cup be far more cooler if each national team had their skin to differentiate them from the others?
Will it be hard for us to create a skin if ever such a system is implemented? No. Go play Armored Core and build any robot, start editing the colours. Very easy, the colours are controlled by sliders and the decal placement is in fixed positions, but for WipEout SL could use a freeform placement like for stickers in LittleBig Planet (Which is easy too.) The only "hard" thing is choosing a colour pattern and decal placement. Oh wow. It makes it even easier than it was in Pulse, with or without Photoshop.
Moderation job for the custom skins can be limited to none, if the skin editor is done right.
And as for the teams retaining their "proper" colour. You'd rather enforce your choice onto someone else than allow them the freedom to choose? Please... I can't help but disagree entirely with that.