I voted Peter because if we are talking in most general terms of leader, as in leader of men, then it's got to be Peter.
When Ender was young, he was a great military leader. A soldier's leader. He was able to lead the smartest kids in the world and manage to avoid any jealousy or resentment and even inspire outright love from his jeesh. However, Ender is not "ruthless" enough to transplant that level of leadership to the political spectrum. Because the simple matter of the fact is, political decisions tend to be a lot more screwed up than military ones. Especially when the former affects the latter. For instance, do you think Ender would ever be able to delay something like the world finding out Achilles' masterplan just so he'd be put in the position of Hegemon at the right time? Of course not. Peter did. That was a bit ruthless. But in the long run, it set off the chain of a course of events that saved the Earth from devouring itself. Peter views everything as chess. Sometimes you have to be willing to sacrifice some of your pieces for ultimate victory. And if you don't play like that, if you try to save every single piece, you will lose. The enemy will win. Ender won decisively against the buggers but only when he thought it was a game. If he were playing with real, human lives and he knew about it, he wouldn't be able to do the ugly deeds in service to the greater good.
And when Ender grows older, he does become a leader of that group of super genius family members that shape the course of the universe, but it's similar to his Battle School in that he can lead a small group of super talented people. That's his niche. He can do that better than Peter, whom Graff mentioned was not suited to military life since he wouldn't respect those above and below him enough. But he's really more a great mediator at that point. Between the family members and the different alien races.
But Peter, he sets up the pieces and makes the moves to favor things his way. Granted, Bean helped out a lot there. But Bean is a military asset. Peter has no skills in that. He simply used the tools he had available at his disposal. That doesn't mean Peter was always on his game and there wasn't more than a few instances where Bean had to bail Peter out, but Bean also bailed Ender out a few key moments, not to mention being the inspiration, albiet indirectly, of the final key decision Ender had to wipe out the Buggers. But just like how Bean could never have done what Ender did, Bean could never ever have done what Peter did. He's just not ambitious enough.
Valentine, now she's a great character, but she's no leader compared to the other two Wiggins. If she didn't have the brothers there to overshadow her, then she'd be a fine leader in her own right. But her role was always mostly to support and provide contrasting viewpoints.
I love Ender's character as much as the next guy but there was just something about Peter's story that I felt really satisfied by reading. He's portrayed so monstrously in the beginning but as you keep reading the stories, it's his story of slowly learning how to join the human race. Some of you disliked the parts in the Bean series where we would be shown Peter in not the most flattering light, doing some not so smart things and whatnot, but I found those parts to endear me more to him slowly and slowly. Because he was learning from his mistakes. And he was learning to accept humility in his life. To not be so damn arrogant.
SPOILERS to the end of Shadow of the Giant:
I just really felt his character made a real complete journey by the end of this book. When his parents tell him how proud they are of him and you see how much that meant to him emotionally. How alot of the bad things he did in his life was not because he hated, but because he didn't feel loved, or as loved, by everyone around him. And when Graff (or was it Rackam) asked him, after they found Bean's missing babies, if they should tell him now or if Peter wants to use Bean more, Peter straight up tells Graff to give the man his babies, he's a good man and he's earned it. That's something the old Peter would never have done. And at the very end, when you see old Peter and young Ender's ansible conversation but from Peter's perspective, a lot of those lines were heart tugging. Peter had the clarity to realize that root cause of a lot of his early faults. But he had the maturity not to hide behind them as justification for everything he did. When he tells Ender throughout his career that he'd always think in the back of his head when he'd make a decision, it was important to him to think, "Ender would have liked that." That was it. I honestly think Peter showed Ender such honesty and emotion that young Ender, still fresh from the memories of "bad" Peter, didn't really know how to deal with, and that's why it took several years for him to write The Hegemon.