Silk Road had the USP - that's where the focus should be. A really well developed free market place running in a Tor hidden service, or maybe making one work in the blockchain of something like NXT.
I think a fully decentralised market could be a money spinner. They need to get away with bonds and holding money on their servers though. It's a bog security risk and only a matter of time before it gets hacked or goes missing.
In general I do not think a thor browser or blockchain powered marketplace will apply to the mainstream merchants and buyers. Thor browsers are for the special interested and general regards to buyers security its not appealing to buy from someone you not can track or find. Would you buy expensive goods from a shop that you new tomorrow is in a other town or country or disappeared....with you hard earned money. What if you not receive, or there is something wrong with the product?
But to create a marketplace that take cryptocurrencies and fiat money, but gives lower rates to trading with cryptocurrencies could might work. But in general the service must appeal to the masses to get reveneau enough to staffing and developement.
it would be a hard fight to change the power balance in the online world. A long and expensive fight. what I think will happen when bitcompanies are beginning to get a big succes, is that amazon, ebay/paypal, google, facebook or other big companies actual buys in or entire companies. Its happened before, and happens again. Bitpay for example will before or later be bought by a bigger investor, why in general. because the investors that invested initially are after growing their money. Thats why the invest in start up companies to have the possibility to grow the money huge.