Alter Self says that it grants the user any racial bonus feats that its new form posesses. I assume that this is meant to apply solely to feats that are already 'locked', such as a declining Elf's 'Weapon Focus bonus feat'. However, Humans get a bonus feat which they can choose however they want. Does using Alter Self to turn into a human grant one this same bonus feat? If so, can one choose a new bonus feat each time they Alter Self into a Human?
No. You also don't gain the elf's weapon proficiencies.
When you alter self into a species, you use the monster manual entry for that species, not the players handbook one.
Those proficiency feats character races gain are not bonus feats, they are the result of the training and upbringing of a sentient species therefore are not a physical characteristic of the form.
Bonus Feats are listed with a superscript B in the monster entries:
Only those monster bonus feats are the ones considered physical qualities for the spell:
You acquire the physical qualities of the new form while retaining your own mind. Physical qualities include [...] racial bonus feats [...]