Hmm, thinking about this some more, how about this approach?

Both alt and control keys do what "alt" does currently.  To get what
"control" does currently, you must use some other set combination of
keys, e.g. ctrl+alt, or ctrl+shift, or alt+shift.  Possibly we could
allow all three possibilities.

I have tinkered a little with it but don't have a complete
implementation yet.  Anyway, what is wrong with this scheme?  It makes
the current control keys harder to access, but hopefully this isn't a
serious problem.  We can designate 26 different hotkeys to be easy to
access; surely with a little rearranging that will be enough?

This scheme will be comfortable to both Windows and Mac users, and it
won't remove any functionality -- only make some functionality slightly
harder to access.  Most written material will continue to be correct,
since alt-based hotkeys get a lot more press than control-based hotkeys.

-Lex