As anyone who has looked at the bitcoin protocol in depth can tell, it is really a huge mess of different encodings, hashing styles, and endian conversions. Although it would be a fairly cosmetic change, are there any projects out there to attempt to rewrite bitcoin and it's protocols to be more consistent and easier to maintain for the developers? (yes, I know it would have to be it's own coin or whatever)
I believe that is what the NXT project is attempting to do.
It is a from scratch implementation of the ideas introduced by Bitcoin et al. They use Proof-of-Stake and claim to provide "built-in support for robust features such as a decentralized peer-to-peer exchange, voting system, messaging/chat, decentralized DNS, and options for instant transactions".