Alignment, mainly causes problems on the requirements end.
These largely weaken and cheapen the alignment, especially for the arbitrary(barbarian, bard, monk) restrictions. Classes that directly draw upon aligned forces are exempt from being arbitrary of course, they do make some degree of sense.
Inconsistent and conflicting definitions of aligned actions:
-The strong bent towards equating Good with Lawful Good(a good number of dishonorable acts get binned in Evil arbitrarily, like poison)
-The bent towards icky = evil(a relic of past editions, where icky = smite-ok).
Shallow interpretations of aligned behavior.
-Assuming characters would be aligned caricatures. Alignment should dictate motivation, and preferred means. Only actual aligned exemplars would be that extreme.
-Law = Stick up the ass. Obeys the law in all things even where laws would conflict. What laws do you follow when your god says one thing, your nation says another, and your current location says a third? What about a code of honor?
-Chaos = Derp, randomness yay! Freedom and individuality are not the same as statistical chaos, and people playing them as Chaotic Insane are doing the whole alignment a disservice
-Good = Shackles. People have a perception that Good bars 'easy' solutions, and it is often used by DMs that way(DMs finding their games spinning out of control would seize at anything, and many characters have Good alignments). So Good acquires a restrictive cast to its stereotype.
-Evil = Psycho. Again, Evil can't have things it cares about, or lesser evils, or social norms.