I think it's very difficult to tell who are really the villains now, other than those whose only want to use their abilities for selfish and often violent reasons. I think that's part of the reason for this volume. Anyone can be either a hero or a villain depending on their intentions. I think we'll find out as the season progresses why certain individuals have chosen to side with The Company, whereas before they viewed IT as purely evil. I find it quite compelling.
As for the use of time travel, I think in this case, the point is to show that the future is not set in stone. Every action causes a reaction...the "butterfly effect"...and we'll have to wait and see which course of action is actually taken and the future that results from it.
On another note, is anyone else curious as to who Gabriel's "baby mama" is?