Metamorphosis does do several things differently than polymorph, although it does give you most of the same benefits.
A.) It affects even undead or construct creatures (ie, nonliving ones). Polymorph only affects living critters. However, it can only affect you, feats, items, and special abilities notwithstanding.
B.) You can turn into an object.
C.) It doesn't affect your ability to manifest/cast unless you're in object form. Polymorph sometimes makes casting almost impossible.
D.) Due to the wording of alter self and how it's referenced in polymorph, you cannot take a form greater than one size larger or smaller than your own. Metamorphosis has no such restrictions.
E.) Polymorph allows ectoplasmic forms. This means that, unlike metamorphosis, you can, ironically, polymorph into [living] astral construct forms (assuming you're a living construct, anyway).
F.) And I believe that's it.