I assume you're talking about racial skill points and racial feats.
I would say you do NOT retain them when you polymorph, but I'm open to being wrong. Mostly I think this way because you gain the racial skill points and feats from your new form.
Alter self lists racial skill points and feats under "physical qualities", which also includes things like flying. burrowing, etc. If you have wings in your real form, and shift into a form without them, would you expect to still be able to fly?
This is different from skill ranks and feats you get from class levels, which you retain during polymorph.