I would actually really love Cyrus to make a comeback, simply because he was a) the most developed of the villains, and b) the one threatening to do the most damage. Team Rocket was only in the business to hurt Pokémon and Giovanni was your typical gang lord, out to make profit; Aqua and Magma wanted to destroy the land/ocean for their own reasons, but Archie and Maxie were never really fleshed out. Cyrus, on the other hand, was completely unhinged by the final Giratina confrontation scene and he wanted to destroy the entire universe, which is a total step up from the others. I think there was a lot developers could expand on from his past - the fact that in Platinum you can talk to three people who knew him as a child speaks volumes for his presence in the Sinnoh games.
Sadly, I don't think he ever will make a comeback. GameFreak are all about moving on with each Pokémon game (that isn't a remake), so the chances that we'll see him again are practically null. :C But still. I would like to know more about him in the game universe. He's also sorta cute in a whacked-out kind of way.