The fact that the Son'a are such open-and-shut baddies from the very first time we see them.
You know, good movie villains trade on ambiguity. Heck, even the Borg Queen had a more justifiable reason for her actions than the Son'a. Even Khan had that little thing about Marla McGivers' death, that gave him pathos and something we can empathize with. What have the Son'a got? Nothing. They're narcissists whose plain motivation is their own well-being. They're drawn as such BAD baddies that it stretches credibility that Starfleet would ever be stupid enough to fall in with them, Dominion War or no Dominion War.
I mean, even if the movie had actually played the old predictable switcharoo and played the Son'a as being sympathetic to start with but only gradually unravel and become more villanous as their real plans become obvious, that I could've accepted. Or if Admiral Doughety had been portrayed as being duped along with the rest of us. But the movie plays the Son'a as villains from the very moment they first appear on screen, and Doughety is likewise painted as a corrupt Admiral. Sure, it's broad strokes. It makes it easier for dumbasses in the audience to understand who the good guys and bad guys are in this movie because they're hitting you over the head with a sign reading "THIS GUY = BAD" all the way through. But good characterization it was not. Good writing
it was not.
When even Riker and Troi's research into the Son'a leads them to wonder aloud why we're in bed with these guys, you know your story has gone wrong somewhere along the way.
I think the problem is in the directing and the music, not the script. I think they tell you "this guy is bad" from the first scene we see with them in the duck-blind. And even with what we have on-screen, I think there is a difference between how Gallatin is treated and how Ru'afo is portrayed. Gallatin is always suggesting how to solve the problem. Ru'afo just wants revenge and is annoyed that the Federation is making him wait for his magic potion. "It's simple. Just get rid of them so we can get on with this." Gallatin eventually does something against Ru'afo. The other members of the crew are just following orders.
This is Starfleet's holy grail. This is taking exploring and technology too far, as outlined in the movie, something also done in WoK. It's a very interesting moral dilemma. And if you wanted a Dominion War movie, this is a reaction to the Dominion War.
Why wouldn't there be xenophobes in the Federation now? Why would we continue to think that space travel was worthwhile? We found the Borg in one quadrant and The Dominion in another. Wouldn't it be nice to go to some planet somewhere and get rid of all this destruction? Are we any better than the Borg, searching for "perfection" at the expense of the culture the people already have?
People are getting lost in the minutia of the movie's logic instead of considering the moral dilemma. The Federation isn't worried about what this will do to the Ru'afos of the galaxy. This is purely about a technological advancement that will give them an advantage and appeal over the other powers in the Quadrant. It is a miracle cure and this asks the question: Is doing a little bad worth a big good?
This movie gets better the more I watch it, the more I put it into the rest of the Trek universe. I wish people would lay off and appreciate it.