Seems to me that pooled mining's vulnerability to DDOS is a key issue to resolve. Pooled mining is a great concept, but it seems that the currencies architecture is/was based on distributed transactions, and a pool creates a single point of failure.
Outside of significant changes to the protocol (doubtful, and would reduce trust far more than the current DDOS irriations), I'd guess that the answer will lie in making pools dynamically scalable via a combination of IPS, load balancing, and hybrid cloud architecture.