Not your post specifically, no. I've seen it often enough that I decided to comment on the concept. In player run games, it's more important, to my mind, that if you must have players portraying villains, that they have no more power or capability than the heroes. They can make up for the balance by actually thinking like smart bad guys and scheming as opposed to being bigger and badder. The heroes will have to work just to catch up to, and counter the villains plans. If the hero is smart, and rarely seem to be, using allies makes sense, but again, it's one of the faults of sandbox in that getting that kinda interaction is difficult.
anyway, I'm just throwing my point of view out there. I far prefer that a GM handle the bad guys as there is no chance of cheating by saying, "Ah ha! I planned for that!" when you're just pulling shit out of your ass to try to make sure you win. The GM can do that, it's his/her job, but unless you want to lay it out out and hope that no one goes OOC, it's too easy to do it off the cuff and counter the hero.