I don't think First Contact messed things up too much. Sure, it muddled with Cochrane's backstory, but in the end they restored the timeline. Of course, that means that in order for there to be warp capable ships the Enterprise has to go back in time and save Earth? That makes no sense. Stupid time paradoxes.
All in all though I enjoyed First Contact, especially the battle for Sector 001. Mmm Akira. It saddens me that there are no die-cast Akira toys or even any official models. I've only been able to find two resin kits, and the good one is now $75. For that price it should be painted.
Enterprise... yeah... don't even get me started.