Of course it's rare, just like FA Cup shocks are rare, it has happened to Man Utd twice and Liverpool also though (perhaps through arrogance, who can be sure?) Recoveries happen against the smaller teams more than you think. It's 'rare' that a smaller team will win against the bigger team by more than one goal and that's very recoverable.
If there is to be a shake-up in the competition it's not going to have the desired effect you seem to think it will for quite a few seasons down the line, you can't undo the amount of money the bigger clubs make within one summer. And without that Champions League money it will possibly be even harder for a shock two-legged result.