I didn't like the silly change to the Alter Self spell. I just don't see it as a poor man's Polymorph, but as a transhuman approach to spellcasting. I house ruled it like this - the caster may gain any one Special Attack or Quality of an Exceptional nature, or may add +4 to any one facet of their character (natural armor), or a +20 to their base movement rate. They may change this once per round but the change takes one standard action to perform.
That way they can fly, or get the armor boost or gain a special sense or natural attack - but only one at a time. The spell physically alters the PC, but does not change their appearance to that of another race - i.e. you look like you, but with wings, or gills, or with a prehensile tail, or thick bony plates, etc.