You and I share a lot in common, Aldo, even in the notion that suggests something along the lines of my old "Koopa Battle: March of the Red-Haired King" (
) idea from a while back.
On the other hand, while a RTS would be nice, I dunno...one of the arguably the most complex genres in gaming seems to be something that I don't think could be adapted for the sake of the kid-friendly "Mario-verse", but so easily. It would probably have to be simplified to something more akin to Sangoku Musou/Dynasty Warriors, and even that might be pushing it. Though it's certainly something I could see Nintendo making so if they and Koei ever got together...
Any way, I have two ideas that could possible work, at least just for the sake of Bowser .
1) M&L3 showcased that Bowser can (mostly) carry himself just fine. I could certainly stand to see that elaborated on, such that he would have to be willing to fight tooth and nail, by his lonesome, for a spell. In the old-school days, Bowser was supposed to be as capable in the way of magic, just as much as he was willing to throw his weight around. An action-platformer-brawler, that played to Bowser's various strengths, would be something I could definitely see Bowser doing well with.
2) The other idea may not revolve around Bowser himself, but perhaps his son.
I dunno, maybe it's me. But I've actually gotten to like the lil bastard over time, ALMOST as much as I like Roy and the original "Magnificent 7". And I think that, like Yoshi in the 90s, it may be only a matter of actually giving the bambino his own title (which is actually GOOD, a la Yoshi's Island) before he really will be able to truly make a name for himself.
Maybe they could do something with him and that Paintbrush again (if he were to ever get it back or make another one). Or he could get something else. I dunno. But I do think that Jr has some potential in him to carry a Mario-style platformer in his own right. Plus, there's always the thing that he's possibly even more of a softy than his old man. If Wario could be made into an (anti-)hero, surely there could be room for Jr to be likewise...