I've always thought "The Voyager Conspiracy" would have worked really well as a DS9 episode. Ignoring the obvious (the name) and that some of the details would need to be changed, I think the basic plot idea would have been great.
Basically, 31 gives Bashir some kind of drug or whatever that enhances extreme paranoiac tendencies and then leaves various bread crumbs that only he can put together implicating some kind of conspiracy between Sisko an the Cardies.
Bashir naturally recruits Garak and the two attempt to piece together the situation.
The twist would then be Sloan knew Garak would be the one person Bashir would turn to and the whole plot was an attempt to get Garak to inadvertently reveal some secret pertaining to the made-up conspiracy.
"Unification" as a TOS episode, playing up the 'Has Spock Defected To The Romulans?' angle to the hilt. Whereas Picard and Data were really just sent along to determine what he was up to, maybe Kirk would feel a greater sense of personal betrayal in Spock's apparent actions; while McCoy counsels him that Spock would never do anything that wasn't logical, but he'd never do anything that would threaten the security of the Federation, no matter what. This scenario could also work as a follow-up (of sorts) to the events seen in "The Enterprise Incident".
I had this same thought as well, even if it is one of the more obvious ideas. Though, instead of an episode, I think it would have worked best as a TOS film. Just the basic plot idea: Spock goes rogue in an attempt to aid a Romulan resistance group; Kirk goes after him would make for one helluva film. But here's the kicker: jumble it up with the best aspects of TUC, and suddenly you're looking at something pretty amazing.
It's the perfect example of the largest problem that persists within the Trek property--it's the whole left hand/right hand thing. It shows how much better the franchise would have been had all the pieces been incorporated better. It's still a huge problem. But I digress...
My point is, it really hurts that the two were released within a few weeks of each other. Surely their production overlapped at some point. It would have been wonderful if at some point Berman could have walked into Meyer's office and say, "I've got this thing. You've got this thing. Let's throw 'em together and go make something." Instead we got was is probably Trek's most boring two parter--never mind Nimoy's salary--and a rather mediocre film.