How did Topher get involved with the bad guys in the first place?
I thought it was obvious that they'd captured him (like they captured Day and the other characters at the supposedly safe compound). I also disagree that Boyd wasn't planned to be the other founder all along, because for all of season one and most of season two his backstory was vaguely hinted at but never explained and with the resources he'd have, it made sense that he could coverup the death of that guy who had Priya committed like he did. It just isn't really explained why he chose to carry out his plan the way he did. As for the finale itself, it's probably the best we could hope for, but yes, it was really rushed and a whole lot of things introduced would have been nice to see actually played out(how did Alpha become good? Therapy? Will? Some sort of tech solution?), and there were still some questions, like what happened to the former head of security guy who got out of the Attic after Echo did? Epitaph One had a flashback of him confronting Adele, but it was left hanging. But I liked a lot of little things in this, and think yeah, it's probably best just left where it is.