Multisig addresses are not useful as-is. External tools of some sort are required.
The reference implementation could be improved to be sure, but it will never be able to be the whole infrastructure for multisig.
As jgarzik notes, there are tools available already that are suitable for infrequent multisig usage.
The thing is, if bitcoind would simply include multi-sig transactions in the balance of each account, this entire problem goes away doesn't it?
A tiny little part of the problem goes away, sure. But not the whole thing.
What would be needed is a general means to monitor specific scriptPubKeys. There has been a lot of discussion on that topic over the last few months. Check the mailing list and IRC logs to see why it isn't a simple change to make.