Being asked "What do you hate about TSLRCM" on the TSLRCM forum feels kinda like being asked "What are your weaknesses" on a job interview - one feels wary of answering too honestly or in too much detail But I'll do so anyway.
1. The changed outcome of Mira's and PC's imprisonment by Visquis.
In vanilla Kotor 2 the PC is freed from Visquis' trapped tunnels by Mira. In TSLRCM this is removed, and Visquis makes the decision to open the tunnels himself. This is stupid. It used to be the player's own efforts freed the PC, which felt good. But in TSLRCM the only reason you don't just die there is that the antagonist is an idiot, which feels unsatisfying, especially since it's not just a "restoration" but a CHANGE to existing story elements. (Disclaimer: this is based on my memories of, I think, TSLRCM 1.6. I'm only starting a playthrough of 1.8.3 but after skimming changelogs I assume this comment still applies.) 2. Saedhe's head on Dantooine.
Of all the decisions to change something in TSLRCM that baffle me, this one does so the most, because it's a simple change and yet obviously wrong, and in no way necessary. As someone earlier said, "He has the voice of an old black man and had a head that matched. Now he has the head of a middle-aged white man."
3. The dialogue added to T3 in the Prologue.
The whole genius of the character of T3 in vanilla Kotor 2 is that he never says a word you can understand, and yet he's got more personality than most npcs in Kotor 1. You infer it all from the tone, context, the reactions of others. I believe this effect doesn't work as well as it used to, if the player is initially spoiled by getting real dialogue from him, and then that is inexplicably taken away for the rest of the game. Besides, the dialogue is incomplete and makes no sense. The other droid's advise is always "fix the problem outside the ship" or "the hyperdrive needs work" - and this depends only on how much he likes you! This makes no sense if you've already been outside the ship and collected parts/mines, and especially if you've already fixed the hyperdrive and just need to travel to Peragus.
Of course this could be improved by making the dialogue depend on the tasks you've completed, instead, and making the option to ask his advice disappear completely if the hyperdrive is fixed. Or add a "use the galaxy map" advice line. Still, the line about "fixing the problem outside the ship" makes no sense, period, because you don't fix anything outside the ship, you just collect parts.
Besides, if this is a tutorial level, preparing you for the rest of the game, then the player should be learning to use the journal to keep track of what needs doing, not rely on an NPC mechanic that won't be there for the rest of the game. This isn't PS:T and we won't have Morte telling us what to do the whole game. Lastly, it feels vaguely wrong to get personality choices for T3 (be nice to the other droid or call him an idiot). T3 is not the PC; his character is set (we know from elsewhere he doesn't approve of being unpleasant to other droids), and there's no need to give him choices like you were going to develop his personality or alignment. So yeah, this is a minor issue, but the addition just doesn't feel like it fits the game.