Being a gay guy, the Vulcan Sex Suits didn't particularly register on me. Shame the men weren't given sexier outfits though.
But the men kept taking off those outfits...
I voted other - wasting a big part of the first 2 seasons in recycling tired old stories instead of doing something original.
Other things that annoyed me, in descending order of annoyance:
The theme song - the only redeeming feature is that I can mute or fast-forward it. (However, the theme of ITMD was awesome.)
Trying too hard to be sexy - the decon scene, T'Pol outfits (more about those later), the totally exploitative episode "Bounty"... It was just a bit too on-the-nose. Sometimes it worked (being sexy, that is), but when it failed, it was ridiculous.
The temporal Cold War went nowhere - but after having seen the endings of BSG and Lost, I'm more forgiving of such things.
Continuity problems within the show (see "Fusion" and compare it with "Stigma") - fortunately, this was fixed in season 4.
Lack of development of some of the supporting characters - something that VOY also suffered from, but Travis was the worst case of it in the entire Trek of a totally undeveloped character credited as a main cast member. However, when you look at how underused and underdeveloped half of VOY cast was, and remember that TOS only really focused and developed 3 characters, it doesn't look so bad. Unless you compare it to DS9.
T'Pol's awful costume in the first 2 seasons - not only because it was too obviously meant to be sexy, but because it was actually really ugly and drab-colored and made her look too skinny. The outfits she had in seasons 3 and 4 were much better.
Things that I don't agree with:
Mishandling of canon - what does that mean?
Acting - it was fine. The show had more problems with writing.
Lack of character development - in some ways more character development than any other show apart from DS9, if we're talking about T'Pol and Archer, even Trip to an extent. It did, however, push some of the supporting characters in the background (Travis and to a lesser extent, Hoshi). TOS had 3 great main characters but they didn't change at all until the movies. On TNG, Worf was the only one with a story arc (though Picard and Data had mini arcs), and the development of characters like Riker and Troi had nothing to do with planned story arcs, it was just the actors learning to act better and the writers starting not to write them so atrociously as they did in the early seasons. On VOY, some characters got development (EMH, Seven, Paris, Torres) but oddly enough, the captain and the first officer didn't - Janeway didn't really change, and Chakotay was pushed into the background; while Tuvok was underused, and Neelix was basically an annoying ill-conceived character who turned into a good character whenever an episode focused on him. Kim was basically what Travis would have been if he had more lines.
Jolene Blalock - I've hardly seen her in anything else, so I don't know, she may be a really bad actress overall; but she was excellent as T'Pol.
Scott Bakula - he OTOH might have been miscast, at least if one expects a charismatic, authoritative captain that people have been used to in previous shows.. But after some time, he managed to get a grip on the role, and in a way, the casting had the effect of making Archer a more accessible, gentler, more ordinary-guy kind of captain, which is actually kinda interesting. He did came off as a fool a lot of times, but I found him kinda endearing
Techology was too similar to the 24th century - well they couldn't have made the technology less advanced than the 21st century! Although I agree that they shouldn't have introduced the idea of holodeck so early.
Certain uniforms have not changed in 200 years - what? Which ones?
