I don't think alignment is neccessarily something that belongs to fantasy settings, but not to modern ones. It is really a system for settings in which you want the characters to be clearly divided into the "Heroes of Light" and the "Forces of Evil". But I argue that this is the case just as often as it is not. And I think there are few cases where it is as clear cut as in D&D.
Especially in works from the recent decade it appears to have become very fashionable to make right and wrong a matter of perspective.

D&D comes from a time when good was good and evil was evil, with no doubts about who is an allie or an enemy. The way it is written, alignment is indeed an integral part of D&D, but a problem arises when people want to play stories that do not follow this bipolar morality. Then you have to get your toolbox open and get to work getting alignment out of the rules and fixing up the holes it has left, so you can play the kinds of story you want.
Which I think some people find quite frustrating. Having an alignment system that is more optional for the game seems to be preferable so those people who want to use it can have it, while those who don't can play without it without running into problems.

For example the half-fiend template of 3rd Edition gives a creature lots of spell-like abilities that can only work with alignment. Offering multiple choices for each level, of which one works with alignment and the other doesn't would take some work off DMs.