I'm pretty sure the Imperial Fleet could take out the Federation fleet. Those ships in a battle just seem to explode so easily, and they're incapable of organizing a defense. But they have the transporters. Way more convenient than shuttles. But the Empire is willing to fight dirty.
Fett could probably wipe out most Trekkies, but I think a good number of Trekkies would be able to do some damage. I think they'd stand a better chance than the average person in a fight, if only for their brains (some). But I've only seen a few hard core trekkies able to exert much in running or fighting.
I like Next Generation and Deep Space Nine. I respect the orginal for its time and some of the stuff the creators thought up. I grew up on Next Generation though. Healthy mix of both Star Trek and Star Wars. I don't think the series' are on teh same level in general. Yeah, they're both sci-fi space adventures, but the actual plot and drive of both are pretty different in my opinion. As one example, Star Wars has more of a mythical feel of something that could have happened, whereas Star Trek is more something of a hopeful future of what might be some day.
But yeah, since Trekkies don't know yet how to build reliable nifty weapons, I'm thinking Fett would definitely be able to take all of them on.