Although my regular campaign group runs a post-Dominion War era game, we have among our players some die-hard TOS fans. So we have come up with a solution which offers, in our opinion, "the best of both worlds" (no reference to episode intended).
What we do is, insert a time travel story every now and again; by the way, amazing how many excuses exist in Star Trek for time travel, voluntary or no. http://www.trekrpg.net/Board/ubb/smile.gif
Our crew has already on a few occasions been propelled back through time...to the TOS era!
Can anyone say, "Back to the Future" theme? Even if you never liked those teen films (you should, though, 'cause it's got Commander Kruge in them..well, sort of. True movie buffs know what I'm talking about), the potential inherent in these time romps should be obvious; you can have that whole "Tribbles & Tribulations" (DS9) feeling, and best of all: in roleplaying, "special effects: cost nothing!
I do feel that locking your campaign on to the TOS is too limiting, even though some whoppers of fun advantages have been pointed out by earlier speakers on this board. I mean, of course it's fun to tackle the original Klingons and Tholians...but even more fun, in my mind, to tackle them AND then to return to the 24th century and meet them again, even see story threads work out over the intervening years!