I've only got four real quibbles with the adaptation:-
1) The music - stock mystical tat for any scene involving elves;
2) The elves wired up to the mains and glowing in the dark;
3) The computer-generated scenery - too much (in minutes) and too little (in variety);
4) All the dialogue cut - particularly between Galadriel and Gimli, Legolas and Gimli, and Boromir and Aragorn.
1) The changed ending did make sense, since Aragorn has a different motivation - he's not interested in kingship, he's scared he'll let the world down by making Isildur's mistake;
2) Aragorn carries a normal sword for fighting with, not just his broken one;
3) Pippin and Merry learning swordsmanship from Boromir and fighting the goblins, so their later exploits are more credible (which they aren't really in the book - you're left wondering where they learnt to use a sword or plan a battle);
4) The ring effects, and bringing Sauron in as an ever-present threat to the ring-bearer, instead of just an empty name as in the book;
5) Removing Tom Bombadil, who serves no purpose beyond making a link between LotR and The Silmarillion;
6) The battle scenes - I'll differ and say I thought they were very well done, as was Boromir's death-scene.
I've no doubt that there will be a director's cut of the film. The worry this time was just whether anyone would watch it - now its quality has been proven, that's no longer an issue. Hang on another 5-10 years. I have to say I'd rather see the director's cut on the big screen than on DVD though!