They could be, they could serve as tokens for shares. i.e. 0.00001btc could represent one share. The problem is you wouldn't have a two way transaction - if you pay first, you have to trust that the person will return the coin. If you send the shares first you have to trust the other person will pay. It might be possible to configure it correctly with the scripts, but then you'd need to be able to write scripts that know about coin 'color'. Which I'm not sure is yet supported. In fact, I'm not even sure what scripting features are currently supported.
My idea would only need normal scripts with data included, that the asset issuer would look for on the blockchain.
Has anyone considered maybe using one of the secure alternative coins (the only one I can think of is Litecoin, every other one is venerable)
Instead of bloating our blockchain, use Litecoin as a coloured coin system.
"Our blockchain" is already bloated with stuff like shatoshi dice. And these transactions would include mining fees, so that would be helpful. And like I said, just using colored coins doesn't guarantee that the shares will actually be paid for. Since I could send a colored coin and then not get payment - the other person would have the colored coin and I'd be boned.
Other then that, my proposed system could be implemented just as easily with litecoin as bitcoin. I think mainly it would be used to move shares between exchanges as well as person to person OTC trades.
With my system, though you could still have an "exchange" where people just post bids and asks along with their addresses, and then remove them when they're filled. The exchange wouldn't actually need to hold any BTC or shares, it would just be like a message board. Or you could write an application that used an IRC channel to post trades, as bitcoin originally did.