I think one of the main issues is the fact that a the main attributes of a healthy exchange (high volumes/deep order books) make it a juicy target for hackers(lots of money in one place). It would seem that one possible avenue would be to have lots of little exchanges which share their order books, thus decoupling the advantages of being big(deep order books) from the disadvantages(juicy hacker target). Personally I think this is one of the potential strengths of the bitshares project.
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I will have to look into the bitshares project some more but you do bring up some very important points here as far as the exchanges with high volumes making them more vulnerable to hackers across the board. Very interesting @lafona