Okay, I've recently learned that most of the benefits of the Alter Self spell in PF come from it being a spell from the Polymorph subschool. The reason I rated Metamorph so poorly was because I had incorrectly assumed that Alter Self (and the Monstrous Physique line) only applied the effects listed in its description: a different appearance, a +2 to either STR or DEX, and possibly darkvision, low-light vision, scent, and/or a swim speed. The stuff about adding natural attacks (like it did in 3.5) is tucked away in the description of the polymorph subschool.
Well, that's a bit of egg on my face.