Disclosure: I work for Coinprism.

Counterparty uses the Blockchain for timestamping only. It doesn't use it as a ledger since it builds it's own "parallel" ledger.

As a result most advanced functionality of the Bitcoin ledger can't work on Counterparty:

nLockTime

SPV

Payment Channels and lightning networks (very important for scalability)

Unconfirmed transaction chaining (important for mobile payments and fast transaction processing)

If you want to be able to use all bitcoin features out of the box, you need to look at colored coins.