You know stuff like that already existed.
Touhou Project, Cave Story, FTL, The Binding of Isaac...
What is different (maybe?) now is that game creators are leaving or getting kicked out of companies and then keep going their stuff on their on.
(Is it what you just said? XD )
Maybe it's a symptom that something is wrong with those companies.
For contrast purposes, it's worth nothing that Miyamoto is still working for Nintendo.
As for whether this continue or not will be up to the game companies themselves giving their creators the conditions they need to make good games.
If they don't, well thanks to various factors now like Steam and Kickstarter, they can go elsewhere.
Hey they could even go on their own if they're willing to. ZUN among a fews other have shown that this possibility is real (although maybe not for everyone).