It really depends on your use case. With the upcoming release it's more and more going to be a tough decision in my opinion.

Do you need a larger community? Use Counterparty. Do you want a stable and fast desktop client or server? Use Omni Core. Do you want bets? Use Counterparty. Do you want crowdsales or bind tokens to arbitrary scripts via pay-to-script-hash? Use the Omni Layer. ... Contracts at some point in the future? ... etc. etc.

There are of course other alternatives, or maybe all this isn't useful to begin with, but I'm mostly comparing apples with apples here.