My idea takes place maybe a decade or two after Nemesis and involves section 31 and the aliens from the episode Conspiracy.
Mine... same general timeframe, but a much more.. unusual... plot idea. But one which shares a few basics with yours...
I think we all agree... the "conventional mustachio-twirling-bad-guy" is no fun. I had hopes that JJTrek would have done a decent villain... Nero seemed like an interesting idea, but ended up barely even 2-dimensional. Khan was only interesting because he was a noble, tragic figure, not just a "twirly-baddie."
So... you've picked up on a thread done in Conspiracy... "what if you can't tell who's who." This is a common element to mine as well... but the force behind it is completely different (and would come as a huge shock to the audience when it was finally revealed, in the final season). See, the "evil alien bugs" is still a bit 2-dimensional.
For me, having a "villain" (only in the most loose sense) who really thinks that he is doing something GOOD... while doing utterly evil things... is much more interesting. AND, by the way, much more relevant to the real world we're living in.
Not being critical... just explaining why I went in a different direction. I've got a story treatment... complete with cast descriptions, a ship concept (and yes, the ship isn't guaranteed to make it all the way through the series, nor are all of the cast members guaranteed to make it through either). I'm a HUGE fan of the level of change, and of REVELATION, which was seen in, say, Babylon 5.
I want a story that literally changes everything... and in this case, in some ways "reverts" the Star Trek universe to a less technologically-obsessive time and focuses much more on the "natural, humanity-oriented" side of things. Star Trek was originally very humanity-centered (and I'm including all the alien races in "humanity"... we just don't have another term for that, do we?) With TMP, we deviated massively from that, however... and that's the biggest critique of ST-TMP - that it was almost antiseptically "anti-human" in many ways. And then with early TNG, Roddenberry fell back into the "let's pretend humans can be perfected" thing AGAIN. And it took several years for the show to recover from that, and while TNG mostly did recover, Trek as a whole became much less "human" in feel over the years.
This is the one "positive" I can throw out about JJTrek... and mind you, I don't think it was successful... but at least he TRIED to make the characters more "identifiably human." He just turned characters I'd always been able to identify with into characters I don't know, and don't necessarily want to know, and absolutely can't identify with. Like with everything else in that flick, he focused on contemporary music and cars and booze and so forth... he focused the trappings, not the core elements.