What is the best Star Trek Series in terms of characters, story, special effects, etc.?
Wow, I have to give multiple answers to this.
For me, a toss up between TOS and TNG. If you count the TOS movies, I have more emotional connection to the Kirk-Spock-McCoy dynamic, but I think the TNG characters had more time to develop themselves, and the characters definitely had more growth.
Hands down, DS9, as it was the most serial of all Trek. That is what was so lacking in the other series, as they were all mostly episodic. DS9 took the groundwork TNG had laid for referring back to previous episodes, etc, and ran with it.
Not counting movies, I thought Enterprise FX were the best, but makes sense since it was the latest. Voyager towards the last few seasons rivals Enterprise, as does DS9.
But if you ask me what my over all favorite trek TV series (not including movies) is, then it is TNG. But it is a close call, as I like all the series.
VOY: B- to C+
ENT: B- to C+