Maybe the high transaction fees problem can be sidestepped by making a clone of Counterparty on a blockchain that uses the same address format as bitcoin so that for each bitcoin address that exact same address works on the other chain; and is merged-mined alongside bitcoin so has a very high difficulty albeit not as high as bitcoin's since not all bitcoin miners do merged mining.

I am thinking of DeVCoin, which admittedly is based on bitcoin code that by now is a little old, but should not be too hard to bring up to date if newfangled features of bitcoin are desired.

Counterparty could even be updated to be able to retain linkage to bitcoin's own blockchain by periodically doing bitcoin-chain counterparty transactions bring the bitcoin chain up to date with various transactions that have happened on the cheaper chain, to pin it all back to bitcoin's level of difficulty/security from time to time.

-MarkM-