I generally find those seasons quite consistent and certainly don't think they have any episodes nearly as awful as the low points of season 3, but there are a few episodes that I found terribly boring and/or too melodramatic or silly to take seriously or find entertaining like the better episodes. There aren't many in the first season, but I did find "The Menagerie" unbearable. I understand they were just trying to make use of the footage from "The Cage" so it didn't go to waste, but I thought they did that at the expense of telling a coherent or interesting story. I also found "The Conscience of the King" rather dull (I can't imagine why someone as smart as Ronald D. Moore would call it his favourite episode), and thought "Dagger of the Mind" started out intriguingly, but ended up being too corny.
While my objections to those episodes are mostly based on finding them simply underwhelming, there are episodes in season 2 that I actually despise, starting with "Amok Time". For the life of me, I can't understand why this episode is so popular. I thought everything that happened on the planet Vulcan was absolutely ridiculous, and a big reason people make fun of Star Trek is because those scenes seem to be in the general consciousness as some of the most iconic and memorable ones in the series. For me, however, they are only memorable for how silly they are. On the plus side, I have to admit I also think that episode has one of the greatest endings in the history of Star Trek with Spock's reaction to Kirk's 'resurrection'.
The other thing that bothers me about season 2 is that a lot of the episodes start off promising, but then degenerate into the kind of nonesense that annoyed me in "Amok Time". The fighting scenes in "The Gamesters of Triskelion were just a rip-off of the Kirk and Spock fight, for example. Of course copying something that wasn't even good in the first place leads to disaster. That's just one example of a problem that started in season 2 that became much worse in the following season - the show following certain formulas like 'the crew visits a planet where people are emulating something from earth's history' or 'some crazy force invades the Enterprise'. After awhile, I got sick of stories retreading these two basic premises.
In the second category, I thought "The Ultimate Computer" was the worst offender - just an overly talky, way too obvious attempt at conveying the message that technology should not be valued over humanity, with a disappointingly grating guest star. This is the supposedly Great Daestrom who is referenced in later series as a man brilliant enough to have an important place named after him? The redeeming factor is that in spite of these misguided episodes, seasons 1 and 2 also had some truly inspired and original episodes with sharp writing and unforgettably endearing and sometimes even powerful acting, unlike about 85% of season 3.