Why would both games suffer if they're handled by different developers in entirely different universes with entirely different styles?
Agreed. They look entirely different, they are marketed entirely different, even the title logo is different, they also probably appeal to different target audiences.
The critical success of DmC and the hopeful commercial success will likely get Ninja Theory another bid to do a sequel. But given that Dragon's Dogma was probably a flop, Itsuno and company need to be working on something. That something could easily be DMC5.
The release of the games could alternate every year or 1.5 years.
As dahbomb said, Capcom did say they wanted to decrease the amount of time between sequels to major franchises. They also are looking at western games and how they garner success, i.e, quick, almost yearly releases of AssCreed games and Call of Duty.
It will cause brand and character confusion. Sort of like MM.
Not if they properly plan, market and develop the games accordingly. Also there have been WAY too many MegaMan games, it goes far beyond a simple two branching entries of a franchise. Furthermore, these different MegaMan games have drastically wavered in quality. MegaMan would be a bad example of putting out multiple series of the same franchise, Call of Duty is probably a better example on how to do it better. Black Ops is clearly the Black Ops brand, and the other is clearly Modern Warfare. There surprisingly is very little confusion even down to the most casual, dudebro mountain dew drinking gamer. It all depends on how Capcom and Ninja Theory approach it.
EDIT: I'd like to also add that these various MegaMan games were all developed by Capcom if I'm not mistsaken, that - by virtua - give those games a similar, 'soul' if you will. There is clearly a massive difference in tone, theme and character between Ninja Theory's Devil May Cry and Capcom's Devil May Cry. It'd be pretty hard to even remotely call them samey.