deleted

[Duke of Urrel]

I think it's a good idea for humans to lose their extraordinary qualities when they polymorph into something else. It's a good idea because it balances the various Humanoid species. Demi-humans (if you'll pardon my use of this term) shouldn't be the only ones who lose something when they're polymorphed; humans should lose something, too.

However, I don't consider the answers given in the D&D Frequently Asked Questions to have the same authority as the rules in the rulebooks. I think many other commenters in this forum agree with this. It is said that whereas the questions asked in the D&D FAQ are canonical, the answers are not.

So I myself have some house rules for what happens when humans polymorph themselves into other creatures using Polymorph spells based upon the Alter Self spell. You're welcome to use them or to ignore them as you wish.

LOSING THE HUMAN BONUS FEAT: I don't consider any one of a human's feats to be more "human" than the others. I also don't like the idea that a polymorphed human should lose not only the first or second feat they ever gained, but also the use of every other feat for which the lost feat was a prerequisite. Instead, I require a polymorphed human to lose only the most recently added feat.

LOSING HUMAN BONUS SKILL POINTS: Likewise, I don't consider any one of a human's skills to be more "human" than the others. So here's what I propose to do if you are a human and you cast the Alter Self spell (or any other Polymorph spell based on the Alter Self spell) on yourself. Add three to your character level; the sum represents the number of human bonus skill points you have. Divide this sum by the number of skills you have. Drop any fraction from this number and convert it to a negative number. The result is the penalty that you must add to every skill check for as long as you are polymorphed, to reflect the fact that you are have lost your human bonus skill points.

I believe that Polymorph removes the base creature's extraordinary special qualities, but doesn't grant those of the new form.

You're right about this. Polymorph spells based on the Alter Self spell cause you to lose the extraordinary special qualities of your natural form, but they don't grant you the extraordinary special qualities of your new form. Only the Shapechange spell does this.