What's suffering about the protocol?
I don't think there is anything critical, but something needs to be done about transaction malleability someday, maybe they can make it a feature instead of a bug somehow. Colored coins need integration into the protocol in a way that it doesn't excessively bloat the blockchain.
What is really needed is good communication between core and ancillary development so we don't get the issues Mastercoin encountered. And when I say communication, that also means money.