We need to get past this line of thinking. Why do companies not say the same thing for the salaries they've paid former employees? "Boy, I wish we could get back the $30,000 we paid Bob between July 2011 and October 2011."
We don't say that because the employee earned that and once they've earned it, it's out of your account and into theirs. Stock, though a different mechanism, needs to be thought of the same way. If someone has worked there long enough to vest that stock, they should have the option available to own that stock. Just because they made the company successful enough to not be able to afford to exercise their options in time doesn't mean we should take that possibility away from them.
Whether or not it was intended years ago when it became a norm, the 90 day exercise window, at this point, is a surrogate mechanism for companies to steal compensation from employees after the fact. That's horrible.