All electronic games based on the sundry incarnations of the d20 system have had to take liberties with the rules, some more than others. The "all or nothing" argument is facile; even the pencil and paper rules state that the game master has the ultimate discretion when it comes to making rules decisions.
Part and parcel with the licensing rights to use these settings (NWN2, Star Wars d20) is the understanding that the underlying rules will be at least recognizable to consumers. They are as much a part of the brand as the setting, and likely, consumers would be upset if they purchased a D&D title that didn't have the six stats, d20 combat rounds, etc.
Re. 20th level max in KOTOR: I liked the limit because it meant that there was enough room for customizing how your character's force powers would develop while allowing your Jedi to remain unique because you couldn't take everything. Given another ten levels, every Jedi would be essentially the same, which I think ruins the point. Also, the designers could only script so many events that would award experience for actions outside of combat. Having a limit allowed the designers to balance the flow of the game, so that players actually interested in role-playing could progress and not be penalized for not taking a heavy combat approach. What I didn't like was that you started as a different class whose level then limited how many Jedi levels your character could obtain. Given that the power of the Jedi classes seriously nerfed any of the regular classes, I thought this was a bit unfair. To the designers' credit, however, the game still remained pretty balanced.
As for KOTOR2, I'm all for the level 20 limit for game balance purposes, not necessarily because this is what the Star Wars d20 roolz sez. Given that the character starts as a Jedi, my only grievance from the previous game is addressed.