I got hooked during Star Trek's first run NBC broadcasts, so it's my overall favorite, though I'm receptive to all the subsequent tv/film spinoffs. Though every incarnation has individual things I like and dislike.
One on-set thing I disliked was the development of a single helm position on the bridge, that I think first appeared on the USS Defiant. I missed the navigator position, even though it was a cost-saving move, because they didn't have to pay an N.D. Extra to sit punching buttons while a regular character had all the dialogue. It made sense to me for the Defiant due to its size, but then it carried into Voyager's bridge too. But when NX Enterprise, set 200 years earlier, had the same single pilot console, I was disappointed. I thought it should have foreshadowed NCC-1701's helm/nav design.