I think the effort should be put into a decentralized stock exchange, not another autonomous one. One where the tickers, issues, portfolios, contracts, etc are all kept in a blockchain type system. The entry nodes are merely market makers much like the real stock exchange, you could also route your orders through a preferred market maker etc.. Your portfolio, balance, etc is not actually stored on any of the sites, but in the blockchain unlocked only by your private key. There is obvious logistics issues to work out here, but I think through the use of PKC and the blockchain system, it is all doable.
I really do love the GLBSE, but it obviously needs alot of work, and the centralization is a blatant problem especially given the politics involved. However, I think the just like cryptocurrency we are in the infancy on this idea and the development of an idea like i stated above is more or less natural progression given what we know about p2p / decentralization and how it has been implemented in the cryptocurrency world.
I would love to get involved in such a project someday and would be willing to throw some resources at it.