There is a critical difference. Concerning immigration law, what Obama is doing is largely doing nothing, or simply refusing to enforce existing law. Even his Dream Act by executive action is another act of refusing to take the steps prescribed by law.
With Obamacare, if that is struck down, he'd have to take many affirmative steps and have the funds to carry them out. And he'd have to win re-election to carry it very far.
With Obamacare, the funds have already been appropriated and authorized. That won't be a problem for the balance of this term.