Part of the reason the rules are so messed up is everyone has their own preconceptions, and few people take the time to hash out exactly how things will work in their game. For instance, in the IRL game I'm in that we play occasionally, slavery is very common and not evil (slaves get a wage and can buy themselves back, are treated well, etc). This is because it doesn't work in the way it did most recently, and more importantly because the DM wants that as part of the verisimilitude of the world without causing issues for good-aligned, or at least non-evil, characters. That's a discussion that HAS to happen or you get really big issues, with players that understand what's going on being really angry at players that are assuming a different model of slavery.
The other issue what I like to call the "Batman Fallacy" (the name comes from
this illustration) - any action viewed from a certain perspective can be viewed as any alignment, but the alignment system views each action as having a single alignment(though obviously some actions are harder to look at as good or evil). Now, considering the huge number of actions characters take, what perspective are we considering their alignment from? How seriously do we weigh each act? Can we count all actions? Whatever. What it boils down to is this: most characters can be considered any alignment, with the correct perspective and actions:
The chaotic sorcerer that kills whatever comes near him? Well, he follows a very set pattern, and patterns are lawful. The righteous paladin saving damsels by slaying hordes of evil orcs? Definitely just killed more things that she saved, and maybe even bystanders. Even Lex Luthor, who stole 40 cakes - that's as many as 4 tens, and that's horrible - could have stolen them because they were poisoned, or so he could give them to starving orphans. Who knows? Does it matter? The alignment system doesn't take into account - can't really take into account - perspective in this way. And, since I love to play Batman-esque paladins, I've had to do a lot of thinking along this line.