Are you aware of this
pull on github (#2577: Treat dust outputs as non-standard, un-hardcode TX_FEE constants)?
I called your proposal a "colored coin" proposal because it is built upon moving satoshis around. At current fees in the default client, moving those satoshis around costs 5430 satoshis. That tiny price will quickly add up if you try building stuff on top of the standard protocol.
Edit: to answer my own question:
Please don't treat micro-transactions as non-standard. A small amount of bitcoins can represent large amount of value in higher protocol layers. Colored coins is just one example.
Could we perhaps just raise the suggested fee on transactions which contain "dust"?
Yup! But it's not a deal-breaker. Upon further consideration, I realized it's just another form of "you have to pay to put data in the block chain" which is fine. It doesn't prevent message-based protocols from working.
But back to this thread: I'm really looking forward to reading the whitepaper!