As an example, Metroid Prime trilogy was made a Retro Studio, and some of the main folks in charge of them left the studio and many of them are now at Bluepoint. The most recent Metroid has been made in Spain by Mercury Steam. Retro Studios and Mercury Steam had nothing to do with the Famicom games.
Sakamoto designed the original Metroid and directed the other 2D Metroids and Other M, but wasn't involved in the Prime ones and was producer of Samus Returns and Dread. But he's the 'PR star' of the series, in the same way Miyamoto is for Mario even if his involvement is pretty limited. Now you mention Kojima, I also remember he also appeared as 'PR star' for Castlevania Lords of Shadow, even if it was developed by Mercury Steam too, and they only saw Kojima three days.
Kojima's team endorsed their initial pitch to make a Castlevania and provided them facial animation tech and some minor feedback, and supported them with PR. That's all his involvement with that project.
To start, having new studios develop games as projects clearly become larger in scope than previously is not akin to ditching the old guard/treating key staff as replaceable, either. (Again, especially when notable key members of the game staff, like directors and music composers, are still contributing as ever.)
This is particularly apparent when notable Nintendo IP lay dormant for multiple decades simply because one of the heads of the old projects is either preoccupied, or "Can't think of a way to innovate in a sequel." (Ugghhh all I want is a F-Zero with both a car and a track editor at once, Nintendo!)
The Retro Studios story is a bit complicated, but if anything, the fact that there's been such a struggle to get a Metroid Prime 4 out makes the case that Nintendo took the leave of staff (I forget the exact reason why they left and will just assume for now that they're in the "not fucking Donkey Kong" audience) seriously enough to put the franchise on hold. It's also, likewise, an example of Nintendo's quality control standards not allowing a subpar product, considering what we can presume to be Bandai-Namco's failures on Prime 4. Either way, Retro Studios is certainly no Grove Land Games or... whoever those guys who made those GTA ports are.
Incidentally, Mercury Steam's current relationship with Nintendo is pretty much because of their Lords of Shadow series, giving them something in common with the Mario Party staff. That said, Metal Gear was always Kojima's baby, and that's a franchise that has not been doing so hot since he left. Though Konami doesn't really seem invested in the game industry anymore anyway, so perhaps trying to analyze their decisions is hopeless.
I'm having a hard time understanding your position.
Ubisoft doesn't look at this as "burning bridges" because so few people bought and played BGE in 2003, making another version of that would likely be akin to throwing money in a pit of fire.
It's like a kid selling lemonade who doesn't make any money because he doesn't get enough customers. He can either sell a different brand of lemonade or he can turn it into a coffee stand. This outrage is coming from the small handful of lemonade customers who are too few in number to matter. The market wants coffee.
When you call Coffee "Lemonade 2", you're not gonna get Coffee fans to drink it.