Got it on my birthday Oct. 31st and beat it on normal Nov 19th at 4:00~A.M. I had to check my journal to remember the dates. I could have had it done faster if November wasn't such a busy month for me.
I don't think they ever intended to turn her into a Dusk since she's not a Nobody but Saix probably dropped it as a threat at some point to keep her in line. The signs of rebellion didn't show up until after Vexen was slain.
Axel said that Dusks don't have memories from before. Perhaps Xemnas could turn him back with a clean empty mind. If that didn't work we know that he still had plan Sora.
Xemnas being the only one able to do it makes a lot of sense when you remember Xion and Riku stopping Roxas from attacking Xemnas. What's the point of Roxas chopping his way up to Xemnas if Xemnas just snaps his fingers and transforms Roxas into a Dusk?
I think it's possible that Lea and Isa were some of the people that the apprentices performed experiments on. It would explain why they originally had planned to betray them. I've never thought Luxord looked like Ansem...
Honestly, the black hair comes from the Devs wanting to set her apart from them...but I think that the "because that's just how Vexen did it" is the best in game answer at the moment.
The difference between those four and Xion and Roxas is that those four chose to be Keyblade masters and risk their lives to protect others. Roxas and Xion were pretty much forced into a terrorist group and treated like slaves.
By strongly wanting to be her own person she got what she wanted. Perhaps you could say "she thinks therefore she exists." I wonder if Vexen anticipated it since he must have been the one who originally made that possible. Since people see her as hooded before they get to know her and Xigbar sees her as Ven maybe her black hair came simply from Xion wanting her true form to be unique from Kairi and Namine, even if she only knew that subconsciously. So you could say Xion has black hair because Xion wanted black hair and Vexen left her with the ability to choose (or black was just what he gave her.)
