Its hard to say. I think Cilan was designed as a sort of humor machine for BW to make up for lack of Brock and changing TR. But in order to maintain his funny aspects (which I think are weird anyway), they'll need to give people a break every now and then, go back to Brock, or do something different altogether. I'm going to say no he won't be in the next saga as a main character, but it's really going to depend on what direction they want the show to go and in what way they want to balance the humor.
I support Save Our Voice Actors, a Pokemon fan group in favor of returning the voice actors in the anime dubbed by 4Kids (seasons 1-8). facebook.com/saveourvoiceactors