If by plot you mean a story that takes an entire season to tell (like say, something involving the villains), then no. I think the best way to go is to have a good mix of mini-plots and regular episodes; something everyone can enjoy. It would be nice if those mini-plots revolved around something other than battles though. If they need bigger plots, then they should just up the ante of the movies already.
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