My initial reaction to the season (and possibly series) finale was quite positive, so it's interesting to note how a second viewing tempered that enthusiasm. While there were still elements that I enjoyed a great deal, particularly the Whiskey reveal, other items seemed to undermine some of the more intriguing possibilities that emerged over the course of the season.
First, the good. I've always been a fan of Amy Acker, and she definitely showed her range in this episode. I've seen some people note that she might have been a better choice for the lead role, but I'm not so sure. I don't think a recast would have resolved whatever issues surround the portrayal of Echo. Those problems are simply a fundamental flaw of the series. The very thing that makes the character exciting to play makes it difficult for the audience to relate to her.
I also liked Alan Tudyk as Alpha. He's so often the lovable, goofy type that his turn as a homicidal maniac is almost a revelation. He manages to pull off the idea of a man with dozens of downloaded personalities competing for control within his mind, and that madness helps mitigate the confusing mess of his motivations.
In terms of Alpha's plan, his interest in Echo makes a little more sense. He became obsessed with her, and wanted to build himself a bride in his own image. His various attempts to force her outside of the boundaries of her "programming" make a lot more sense now, as do the details of Alpha's killing spree.
The problem is that Echo's journey was supposedly mirroring Alpha's journey, with the implication that her popularity had resulted in so many imprints that something was going wrong. It was long hinted that it was a part of the process that hadn't been well-understood or explained yet. I liked this idea that the technology was a bit beyond the Dollhouse's ability to control it.
Instead, Alpha's violence was attributed to his original personality coming out, despite supposedly being removed. It fits in a general sense, but it seems a bit too pat. It absolves the Dollhouse of creating its own monster if Alpha was a monster to begin with, just waiting to emerge. It does bring up some questions about the recruiting process for the Actives, however.
November seemed to be an actual volunteer. It's been hinted that Caroline was coerced in some fashion. "Man on the Street", "Needs", and "Echoes" all pointed to the notion that the majority of the Dolls have been forced into service in some way. So why does Caroline emphasize the fact that she's fulfilling a contract and has to stay in the Dollhouse? It seems contradictory. (On the other hand, Caroline's situation may be more complicated than it appears.)
Far worse, however, is Paul Ballard's decision to sign up with the Dollhouse administration in exchange for November's early release from her contract. After trying so hard to expose the Dollhouse and save Caroline, with no explanation for why he was so focused on her, why would he work for these people? Just because of the situation with Alpha? It doesn't make a lick of sense.
In the end, Echo ends up in the same position that she was in after a couple of episodes: vaguely remembering someone named Caroline. And with Alpha still at large, there's no real sense of a season arc coming to a meaningful resolution. For that matter, I didn't get the sense that there was a compelling direction for the story to take in a second season. For all the various facets of the premise still unexplored, the show feels like it has already run its course. Considering the fact that this impression came during a second viewing, as opposed to the first, that's not a good sign.