Story aspects (I will refer to future Cole as Kessler and present Cole as Cole):
Moya was definitely FBI, Zeke said he'd researched it. I think it was John who was lying. Either that, or they just happen not to know each other. Or Zeke's an idiot. Any of those could be true.
The time travelling ability- I guess he turned on a substation 
Well, the sequence of events would have been different if Kessler hadn't gone back in time and given Cole the Ray Sphere. I'm not sure how Kessler originally got the powers from the ray sphere, though. That should be cleared up.
Cole's probably reconciled with Zeke. I'm playing through on Good now, and on my evil playthrough, Cole pretty much hated Zeke, but Zeke didn't seem to hate him.
I'm also wondering about Sasha. How did Cole know her before? ("Sasha was a piece of shit before the blast") And what is going to happen to her next? I believe she was Kessler's girlfriend.
I think the monster that Kessler spoke of is Cole. If you are evil, you become the monster, and a good Cole fights you, and the opposite if you are good.
As for the actual game, I think the graphics need improvement, especially the animations. A lot of the glitches need to be fixed. Other than that, not much. More powers, a sense of being able to own something, and of course more missions is always good (though I thought inFamous was more varied than most games). Also, a larger open world.
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