What I don’t like about the first KotOR is that the skills points distribution is far too limited unless you’re playing Scoundrel, a problem that was fixed in the following game.
I have a problem with the way the influence system is set up in KotOR II. Wether you choose to accumulate positive or negative influence with your companions the end result is the same, which is: they tell you more about themselves and in some cases you can eventually train them in the ways of the Force. That doesn’t make any sense to me. Look at it this way: I dislike you so much that I will now tell you more about myself, and eventually, I hate you so much that now I want you to train me in the ways of the Force. Huh? No relationship works like that. It’s why, whenever I play KotOR II I always make sure their moral alignment reflects mine, even if means unwanted dark side/light side points depending on which path I’m setting for my character, plus it adds another layer to my character, as I’m basically manipulating some companions into ditching their own convictions and start to see things my way, which I’m sure Kreia would very much appreciate.
Now the one thing I don’t like about both games is how the dark side transitions look like. You’ve been barely immersing yourself in the Dark Side for a few months at most within the games’ timeline and already you look like a decrepit corpse. I always install a mod in the first KotOR game where only my character’s eyes turn yellow, but when you’re on the path to the Dark Side in the second game many characters will comment on your change in appearance, so I keep the DS transitions as they are, but I still think they are too extreme, with your eyes, hair and skin turning grey. The only Dark Side transitions that were done right IMO are Bao-Dur, Handmaiden and Mira, with Bao-Dur having facial tattoos similar to Darth Maul, Handmaiden wearing black clothing and dark make-up, and Mira’s hair turning a darker shade of auburn, her skin turning pale with visible veins and dark make-up in addition to the characteristic yellow eyes. Atton and Disciple on the other hand look far too decrepit. Maybe I should join the Deadly Stream forums and suggest something along those lines.

Those are all my major complaints about the games.