Future's Past and Echoes from the Past were both console versions of "A Final Unity" on PC. If you want the definitive story, play PC 'A Final Unity' if you can find it. It would take a bit of work to configure Dosbox though. Sadly, this game doesn't seem to be on Gog or Steam the way TOS' 25th Anniversary and Judgment Rites are.
I agree that the DOS version is the most 'complete' version. It certainly wins in presentation hands down. But I find there are bits that are just too clunky to play. And the away missions and space battles hold up better in the console versions.
And, yeah, the DOS version is a real PITA to get working because you need to affix both CD and core speeds and even then it's prone to crashing during videos. It would be nice if it was on GOG, but I think it might be a licensing issue with SpecHolo as I think the only games they have on there is the Falcon series.
Of the two console version, the Gen/MD version is definitely better. It had a later release, so it received a lot of bug fixes. Plus there all the typical issues in any Gen/Snes head2head: higher res, faster processing (which does matter in this game), and less censorship (of which there was a bit in the Snes version.) But of course, the Snes has much better sound effects. (The phasers sound like crap in the Gen/MD.)
Any way you go about it though, the game definitely doesn't hold up compared to the usual 16B classics, but there's still plenty of fun to be had for any [TNG] Trekkie gamer. And, hopefully, GOG will put out the DOS game in prep for the new show.
The DS9 name game, however, is really nothing special. It's just a DS9-skinned cinematic platformer -- and not a particularly good one. It's really clunky and the story isn't particularly interesting. And there's a whole lot of aimless running around.
Like all the cin-plats of the era (Well except for PoP, I guess, but that was more of a case of which was the least worst port. But I digress.), the Gen/MD blows the doors of the SNES version, as the latter has serious slowdown issues at times. And the Gen is just all around more zippy and snappy. Again, it's probably worth a play of DS9 Trekkie gamers, but the big caveat here is cin-plats can be a bit of an acquired taste. If you're not really into them, you might just find the game frustrating.