It's been a number of years since I submitted my first post in this thread, so I guess it's time for me to provide an update.
TOS is still my favourite Trek series, and for pretty much the exact same reasons I mentioned far up above. DS9 comes in second, TNG comes in a distant third, and TAS ... *shrug*
Still haven't seen -- and still refuse to see -- VOY, ENT, and Abramstrek.
Sisko is now my favourite Trek commander (It must have something to do with his awesome voice.).