When you cast alter self and assume a new form, you aren't you any more -- you're someone else. You can change gross physical qualities, significant physical qualities, and minor physical qualities. You need not keep crippling injuries that aren't represented by damage to your hit points or ability scores, unless your DM invents that requirement.
Some would suggest that this is a lot of power for a level 2 spell. They're right. Alter self is commonly understood to be inappropriately powerful for its level.