Really, I think Obsidian is downright awesome, and any issues in TSL (of which there are a lot) come down to Lucasarts pushing Obsidian for a holiday release. Really, Lucasarts is a downright ****ty company in my opinion, but unfortunately they hold the rights to Star Wars. TSL's story, though incomplete, is better than KOTOR 1's. My problem with KOTOR 1 is that it's a generic, cliche big-evil-guy-building-a-big-superweapon-zomg. TSL's is more subtle, makes more sense, and is generally much cooler. I love how Kreia brings in the idea that there is more than Light and Dark.
The main issues with TSL are
1) Bugs, which can be fixed by various mods
2) Difficulty...e.g. the game is too easy to do. Regardless, Beancounter's difficuty mod fixes this.
3) Incompleteness, which should mostly be fixed by Team Gizka.
Unfortunately that so many issues must be fixed by third parties, but once again, I blame Lucasarts.