I would think, or at least hope, that it will. All the changes made to them seem to indicate that they have (or had) something big planned for them, and their new serious/competent nature would eventually lead them to be promoted further to the point that they get actual new (instead of just recolored) uniforms and have legions of Rocket grunts under their command, only to hit rock bottom and get arrested. Then they would join with Satoshi and co. to help bring down the entire organization, concluding with Satoshi battling and defeating Sakaki himself. Bringing in some of Satoshi's old Pokémon like Lizardon, along with cameo appearances by some other pre-BW characters (Takeshi and Kasumi, anyone? ) would only be appropriate to reinforce the significance of this.
Though I'm well aware of the whole games=/=anime thing, I feel it would've been more appropriate for the Rockets to be disbanded during Johto. That would've helped the "fresh start" feeling of BW tremendously.