I think that a lot of people use the alignment system as a restriction on characters and that's why people don't like it. It doesn't have to be that way, you simply choose a starting alignment and then play your character. The only time alignment should be restricting is selecting a class/prestige class, spells, feats, and lawful characters. And even with Lawful characters you can choose to just say "screw this!" and go with a different character path.