With Brock, there was some "evidence" that he was becoming more and more of a marginal character each season (battling less often in comparison, catching/evolving fewer Pokemon. What, by the end of last season, he only had the same 3 Pokemon he'd had a while with just one more evolution of a team member?) Not only that, but it seemed as though this was just the tail end of a continuing trend.
Has there been any "evidence" of a Team Rocket decline? Do they have any fewer Pokemon than normal (keeping in mind that they never got that many party changes to begin with)? Have their battle appearances declined? Have they not done as much comic releief as past seasons? Have any of these points been in a recurring pattern over multiple seasons?
If you see the answer to this as "yes," then please provide the evidence and I may start to think TR may be leaving. Their apparent "promotion/bigger role" may be their last big thing before departing.
If you see the answer to this as "no," then they are more likely to be sticking around. Their new outfits and apparent "importance" in Best Wishes would be a revamping of their formula rather than a sendoff.
I personally do not see any evidence of a pattern of less importance as the seasons passed (they were basically comic relief/ random excuses to have Ash's Pokemon battle from the start). If anyone, however, sees evidence of decline I may have missed, feel free to post it. I may have missed something. As it stands now, however, I think they're staying.