The interesting thing about building on top of the bitcoin protocol is that it doesn't really matter if it is a good idea or not - there's really no way to prevent it from happening. Therefore, it will happen if someone is willing to pay the tiny price of having their experiment encoded in the bitcoin block chain.
Also, my paper is not about colored coins, although the same arguments apply.
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"?