Snapdragyn
Explorer
Unfortunately, everything they've said to 'clarify' polymorph & wild shape in 3.5 so far has only served to further confound the issue. In addition to the aforementioned 'you lose racial bonuses except when we feel like saying you don't' bit, consider the recent Ask the Sage response (now in the official FAQ) which claims that there is 'no reason given in the rules' for someone not to take a templated form. Um... except that there is, in the line in alter self (from which all higher level shape-shifting spells derive) where it says you cannot take a templated form.
*sigh*
*sigh*