let's say each BTC address submitted shares with a risk score associated with it as noted a few posts above. You could throttle the risk score to the users hash rate in a manner that would match (a) the availability of the smaller coins and (b) the pool configuration, ie 5 servers running 5 switching algos with a different (but possibly overlapping) basket of coins). As you say (b) is done already.

The difference I'm suggesting is that the profit/risk factor is user selectable, rather than at present all the earnings got into the pot and are shared equally. It would be a way for the whales and minnows to live together happily, subject to the constraint of the availability of small coins to mine.