* Note, I am not involved in ST, so Wuffle's Law does not apply.
First, the movies. Y has ST II: Wrath of Khan first, which is indisputable, but ST VI Undiscovered Country before ST IV: Voyage Home? Really? I guess one can debate that, but ST: The Motion Picture deserves to be last for the simple fact that this slowest, most unoriginal, most boring Trek movie should have killed the re-birth of the franchise. I dare anyone to watch the movie again. Ug.
Second, the TV series. He has Next Generation > Deep Space Nine > Voyager > Original Series > Enterprise. Really? Voyager is better than Classic Trek? I dare anyone to name an episode of Voyager that they can remember by name or even by description. City on The Edge of Forever, Let that be Your Final Battlefield (a standard for my ethnic conflict classes), Naked Time, Trouble with Tribbles, Devil in the Dark, Amok Time, Omega Glory, and so on. Sure, there was heaps of cheese and some truly awful (Spock's Brain), but many thoughtful, interesting, challenging episodes. What do I remember about Voyager? That it was damned annoying. Next Generation had better acting and effects than the Original Trek, but its length meant that it had uneven parts, like whenever the writers got lazy and had a holodeck adventure. One ep of that would have been fine. Having the occasional B or C plot would have been fine, but way too often it was used because writers were lacking in imagination. A mysterious but wise bartender? Um, ok. DS9 was excellent most of the time. Enterprise? I stopped watching after a few episodes, but it apparently got better. My ranking would be Classic Trek for its highlights and not for its Spock Brain-iness > TNG (which took about two seasons to figure itself out, just remember how Troi started out) > DS9 (bonus points for Quark) > Enterprise (because it caused me less pain) > Voyager.
Third, the Episode rankings is just wrong in so many ways. Four of the best ten are Voyager or Enterprise? I think not.
Fourth, villians. Q was heaps of fun, and Gul Dukat and Khan were epic in their ways. I actually think the Borg are over-rated. Started out good but got over-used. Lore? Really? Evil data? Thanks but no thanks.
Fifth, best crew members: the list here is Spock > Data > Worf > Kira > McCoy > Riker > The Doctor > Hoshi Sato (?) > Geordi > Dax. Ug. The top five are probably right, although one could reorder them a bit. Riker? He was pretty vanilla until the last couple of seasons, if I remember correctly. The Doctor? Yes and no. The actor was great and snarky, but the premise and then how he got used? Not so much. I think the list is missing one Scottie, is it not? I would change the bottom five of this list to be Scottie > Dax > Odo > Geordi > the average of Sulu/Chekhov.
No ranking of the Captains? Picard > Kirk > Sisko > Scott Bakula (for Quantum Leap street cred if nothing else) > Janeway.
Update: I caught my typo but so sad that my fingers typed work and not Worf at first. Probably guilt-induced.