Well KOTOR2 just have too many ridiculous stuff in it (plus a disappointing ending) to be on par with KOTOR.
The ending did sucked ass I agree but I found the moral dilemmas and the greyness of everything to be even done better in Kotor II and I just enjoy it more than the first one. Also the combat is better.
Of course it has some nice moments but overall it is just not on the same level as KOTOR. SWTOR on the other hand I would say is for the most part on KOTOR level.