I agree with pretty much everything people have already mentioned. But I have a few other ideas.
Kotor1: More benefits from using other characters, aside from story points. I mean, you can basically cruise through the game with Bastila/Jolee and Juhani. And Mission calling Zalbaar "Big Z" all the time sounds kinda creepy.
Kotor2: Expand on the "healing" your Force powers plot. For example, travel to different places with Force strong areas (like the cave Luke went into on Dagobah) or visiting alternate Force using groups, such as the Baran-Do Sages or the Witches on Dathomir. Also, more tie-ins with Kotor1. You get T3-M4 and HK-47, and you see that Carth is still kicking, but what happened to Juhani and Jolee and Mission and Zalbaar and, heck, what is Revan doing while the Jedi are being hunted down by Sith Lords? You'd think he'd go "That's not right, yo" and start kicking Sith butt again.
Both: More to do with the naturally dark side characters, like Canderous and HK-47. There's really no point in doing anything with them except for Hanharr in Kotor2, but that's minimal at best. HK-47 hints at content that was cut when he mentions finding the HK-50 factory so I guess there WAS more to those characters. I'd really like to know why Obsidian absolutely HAD to rush the game out and why Bioware even handed off one of their best games for someone else to basically ruin. There was at least one game that I remember was delayed for several years, up to the point that rumor was that the game was dropped, but it finally came out and it was great. Ok, rant over. I would have liked to see different Force powers, maybe even countering powers. Personally, I liked Force Absorb and Force Destruction from the original Jedi Knight and the Mysteries of the Sith expansion. And by countering powers, I mean like what Yoda did in Attack of the Clones when he caught Dooku's lightning and threw it back at him.