Keep in mind SE also includes Eidos (Montreal, Crystal Dynamics, IO, etc) and whatever's left of Taito. They're like four companies in one.
Reminds of that weird rumor they were looking at Hino for pres.
Level 5 would definitely mesh better, Nintendo already publishes most of their library overseas, but I think there's something to be said for the diversity Capcom would add. Competitively too, locking down Monster Hunter and locking out Resident Evil and Streer Fighter from Sony/MS could be a big deal.
The problem with Capcom is while their IP diversity will be totally beneficial for Nintendo, the fact that many of those IP have also been damaged by certain bad moves is not going to be a good thing.
DmC happen, Megaman is dead, Resident Evil is loss, SFV killed SF, LP3 killed Lost Planet, Dragons Dogma is too expensive to be continued, BoF mobile tarnished the IP..... Hell it is actually easier to mention what IP they had left which is still going strong. MH and Phoenix Wright and sadly no more.
Not to forget the bloated number of Capcom employee and their high turn over rate is going to scare the hell out of Nintendo who surely don't want another Retro studio problem.
Level-5 on the other hand is what Nintendo should strive to become. With only 280 employee, the number which is only double of Hal Laboratory,or triple of Game Freak, they had produced so many hits that it is not even funny. While they had some blunders/flops like the infamous Gundam Age, Time Travelers and Girls Rpg.
They had been keep pumping out greatly succesful IP every generation. Layton series, Danball Senki series, Inazuma Eleven series, Fantasy Life and of course the absolute phenomenal success Youkai Watch series.
As long as they had Nintendo to give them brakes on how not to run their IP to the ground, i can see how they will both really supporting ecosystem.^~^