Well, alignment in itself is a needed concept considering how much of the genre falls within 'epic battle of good and evil', so the mechanics must be able to support this need. Not all games have such a focus, so the alignment rules must ALSO be sufficiently detachable from the system.
Unfortunately, the rules for it are poorly done and the allocations often arbitrary. Add to that the issue of many aligned effects tending towards horribly broken(the BoED and BoVD have added 'much' to overpowered effects)...I can certainly see why many would rather do away with it entirely than try to make it work.
Biggest beef, most clerics and paladins follow a god, who has a code of conduct(might not be very strict either, for quite a few of the even tempered ones). Gods' code of conduct does not equate to aligned code of conduct, as the behavior of deities in fiction and mythology prove. Clerics are by default, strongly good/evil(with a passing nod to neutrality in that they 'can have the option to follow either).