the obligatory 0.0001 transaction fee is a bit of a pita for playing around with these colored coins,
which are only 0.000006 each
0.0001 BTC is only four and a half cents ($0.045). The transaction fee is a deterrent from creating a bunch of spam transactions, so it is a very good thing.
In a practical setting, the value of the "color" transferred should be much larger than the transaction fee. The fact that only 6 bits actually got sent is not the point. The point was to transfer ownership of the digital assets.
It typically costs over $100 to transfer assets such as shares between brokerage accounts--that's at least 2000 times more expensive than transferring shares using open-assets.
I am still a bit confused about this. If I transfer 1000 shares of ABC stock, will the underlying bitcoin transferred be 0.000006 or 0.000106 including the transaction fee. I would think the transaction fee needs to be included.
Here is an example of a colored coin transaction.

I think the 6-bit input from 1MdTq is the "colored coin" and the other input is the uncolored bitcoin "fuel" that makes the transaction work. You see that there are 4 outputs: two 6-bit colored coins, change, and OP_RETURN metadata.
One of the colored coins got sent to 1CcG, the other was returned as "colored coin change" back to 1MdTq. Since all colored coins are 6-bits, this required borrowing 6 bits from the uncolored bitcoin fuel. 100 bits was also paid out of the fuel as a transaction fee, and the rest of the uncolored bitcoins were returned to 1MdTq. The OP_RETURN logs metadata to the blockchain that records the accounting for how the "color" in the input colored coin was split up into the two output colored coins.
