Agreed on that they're flawed games with good elements. However, I think Bloodlines and BG have higher highs than KOTOR, and about the same lows so I rate those two as better overall (but I don't think any are masterpieces).
What ways did you find Bloodlines better than KOTOR? Combat and character building are bad in both games, but worse in Bloodlines. Both suffer from the cramped locations of modern RPG's, but Bloodlines is even more cramped than KOTOR. Bloodlines is basically on rails, where there are many locations you can't even return to after you complete the mission there, and much more gating (you have access to one hub, then the next, then the next, etc.).
The KOTOR isn't particularly interesting, but it works with how the game plays out - you're trying to take out Malak, either because you want to replace him as a dark lord, or because you're a Jedi now and want to defeat the Sith. Bloodlines has a incongurence between the story and the game. It presents the setting as a political struggle between different vampire factions. The Anarchs are trying to get you to join them, Strauss talks to you about supporting the Camarilla over the prince, you can get friendly with the Kuai-Jin, etc. But then the player is forced to work for the Prince and do everything they say right up until the very last mission. When I got the sarcophagus, I tried giving it to Strauss or the Anarchs - no dice. I have to give it the Prince, only to turn around and fight through the building to take it back from the Prince. Except the player doesn't even do that, because after fighting to stop the Prince from getting the sarcophagus, he...gives the Prince the key to the sarcophagus and then walks away...?
There were a few interesting missions in Santa Monica. But after that, the missions are pretty mediocre.
The only thing I think was really good about Bloodlines was the atmosphere. It's a very style over substance game. The Codex likes to complain about walking simulators, then gush over the haunted hotel in Bloodlines, which is a long extended walking simulator sequence with zero gameplay (and that the game forces you to go through each time you play).
KOTOR has plenty of flaws, many of which are similar to Bloodlines. But at the end of the day, I feel like Bloodlines has many more flaws.