The grammatical pedant in me is compelling me to say that, strictly speaking, two-season shows should be excluded, since the word "best" can only be used for comparisons of three or more things; in comparing two, you can only say which is "better."
But now that I've gotten that out of my system and appeased the inner pedant for the moment, feel free to ignore it. It's kind of a silly rule anyway.
Let's see, I'd have to agree with Enterprise's final season being the best. I loved its innovative use of variable-length storylines ranging from 1 to 3 episodes; it was a great middle ground between episodic and serial approaches and gave them a lot of flexibility. It's a format I'd love to see repeated elsewhere.
As for SeaQuest, I didn't care for the final season at all, but then, I found the first season largely mediocre and uneven, and the second isn't even on the table. Mainly I didn't much care for the new, darker format and characters, but I can see how some might prefer it.
I don't agree about DS9 either; I felt they dragged out the Dominion War arc too long. Both TNG and DS9 were kind of showing their age in their final year or two, and were strongest in the middle.
I wouldn't say it's the strongest, but Voyager's final season (run by Kenneth Biller) was a step up from the previous two (run by Braga). The writing was better, there was more progress in the storyline, and the characters were allowed to evolve in ways that they weren't in the previous couple of seasons. But "Endgame" drags down the average.
I'd cite Power Rangers if it weren't back in production now. Power Rangers RPM was by far the best season to date. But it won't be the last season for much longer.
I think that each of X-Men Evolution's seasons was better than the previous one. It started out as a pretty dull "superpowered kids in high school" show, but with each season finale, the stakes got higher and the stories more epic. The show really came into its own after the second-season finale, when the existence of mutants was publicly revealed. Keeping weird stuff secret to preserve the normal status quo is a pervasive trope in SFTV, but it's so much more interesting when the secrets come out and do affect the world. I think XME had a shortened final season and was given a rather abrupt ending, but I daresay the last was the best.
Which reminds of The 4400, one of the few shows that made the weird stuff public from the get-go and really embraced the exploration of how it changed the world. I'm trying to remember whether its final season was the best, and I think it was in some ways, in terms of the epic quality of the evolving narrative, but disappointing in others due to cast departures and annoying aspects like the Cassie character.
