Well, both platforms require you to use a new currency (ether and XCP currency.) Counterparty will make it easier to write contracts that involve bitcoins (I think, not totally sure how that works) ethereum will have a 12 second block time vs a 10 minute block time (very different) and ethereum transaction costs should be lower (for several reasons.)
Additionally, counterparty will probably launch their product first.
Also, ethereum is only one piece of a much larger technology stack being worked on, linking contracts to things like private messages between users, a file distribution system, a webkit-based webrowser/wallet system, etc. Additionally, ethereum can support SPV, a technology very relevant for mobile apps, which apparently isn't possible with a XCP-type system.
(Counterparty also has add-on technologies, but I'm not that familiar with their stack.)