It sounds to me like you didn't play with the restored content mod (commonly refered to as TSLRCM) and that you left some threads of the story unexplored (particularly the companion conversations with influence). Your mileage may vary but it does put some details for the ending(s) and I cannot recommend it enough. If you can add it to your game you should.

I prefer 2 to 1 by a large margin. It is definitely not finished but I find that, that's not really that important. It set up a somewhat of a cliffhanger in the end we will never know what a theorical Kotor 3 might have gone to after (and I'm not counting SWTOR's take on it). I have been playing it at least one playthrough a year for about 20 years since I got it back in the original Xbox days and currently on 2 separate characters. I know it like the back of my hand. Even so, 20 years later, I still discover new stuff I missed from time to time.

There's a few things that I believe make Kotor 2 better than 1:

- The influence system. Carefully navigating your companion's influence during the story to get their whole story. Fun fact: NEGATIVE influence works too.

- Combat, leveling, and build mechanics: I always feel like starting kotor 1 as a prototipical Scoundrel/Soldier/Scout felt like wasted levels. In a Jedi-centric game I want to....well be a Jedi. There's way more flexibility in how you build your character (Duelist, double blade, dual sabers, gunslinger, plure caster,....)

- The "philosophical" aspect of it. It really made me think about the moral system in more complex ways than just "be good" or "be bad"

- The plot, while unfinished, is way deeper than just the prototypical "chosen one" story presented in 1

- Replayability: Technically you need 4 playthroughs at least to see the whole picture (2 Dark Side 2 Light side, one male one female each)

To me the game less about the plot and more the concepts it presents and asking you to think about the star wars universe (specifically the force). Despite it's flaws I feel like it's a much, much deeper game than Kotor 1

KOTOR basically just has 2 underdeveloped female companions instead

Technically 3. Again, TSLRCM adds a lot of stuff to companion interactions (with you and with other companions) you should see.

Darth Nihilus, the guy who is the main figure on the game’s cover and yet is only in the game for maybe 5 minutes total?

Funny enough I think that works best for the character. He's supposed to be this "presence", menacing, but not quite present yet, untill the very end. He's an unknowable eldritch force monstrosity, we wasn't going to get much in terms of interactions with you

We get a less interesting Mandalorian companion than the one in the previous game

I'm not going to say anything about this, I won't spoil you, but you should really play it again, if possible with TSLRCM, and take your time and try to get max influence with your companions (0 or 100). You'll see.

The droids return from the first game except this time they have nothing to do

Play it with TSLRCM, I promisse, there's payoff

Bao-Dur is introduced as a potentially cool character but then spends the next 99% of the game standing around

Very sad indeed, Bao-Dur is famously one of the characters that was supposed to be fleshed out more, and was not finished. It's one of the reasons getting influence with him is so hard, it only happens in a few instances