For TNG I was thinking Time's Arrow. Versions of the Enterprise bridge crew, an AU version of Data that's also a persona of Data's Head and Data's Body, Wild West San Francisco time location and hopefully some more native characters from that time period including Mark Twain version of Samuel Clemens. Some cards from First Contact wouldn't hurt either.
For Enterprise I was thinking a focus on the Carpenter Street episode. But that would require the Xindii Affiliation to give characters and objectives from the flip side of the coin. (I'm going to avoid the Storm Front storyline since that was an alternate timeline).
For DS9 I was thinking of a focus on the episodes "Past Tense (Parts 1&2) and "Little Green Men". A dual personnel of Kira and O'Brien that can report to any Earth time location, and time traveling Ferengi come to mind. For TOS I'd suggest missing elements from "The City on the Edge of Forever". Trials and Tribblations could add a few cards as well.
For Voyager the "Future's End" story arch is a no brainer. Rain Robinson, Starling, the Timeship Eon, two versions of Captain Braxton, hired thugs and the main characters incognito via 1990's attire. For the TOS Movies it's got to be missing elements from Star Trek IV including a "Sling-Shot around the Sun" or "Time Warp" card and a joke about guesses. And some cards from Flashback wouldn't hurt either... Janeway? Anyone? No?!
Of course, this all just speculation and brainstorming. I think they're done doing blocks for a while anyways, but it's fun to fantasize (and much harder to create all of this stuff).