On the Wii you just connect a GameCube controller (first or third party), problem solved.
And since the controller layout of the GameCube is very similar to any other modern controller (Xbox controllers, DualShocks 1 - 4, Wii U tablet controller, Wii U Pro controller, Switch Pro controller, Switch Joycons...), I'm sure Nintendo would figure it out to make Super Mario Sunshine HD compatible to the different Switch controllers. If users of emulators can do it, Nintendo can do it, too.
The Super Mario Galaxy games already officially support normal game controllers on the Nvidia Shield console... so there would also be no problem for Nintendo to port them on newer Nintendo systems like the Switch. Additional the JoyCons have motion controls, so a Switch version could offer both input methods.
The "heavily link" between 3D Mario games and their original hardware and controllers are much less important than you suggest.
It's not about resolving any issue, connecting a Gamecube controller implies that you have to buy one in the first place cause BC isn't complete (that's what I did for eg). And it doesn't work if you have a Wii post 2010 or a Wii Mini (which both lack of gamecube controller ports).
You must know it's only the chinese Shield can play Galaxy. You can also add that SM64 was released on the iQue Player then.
Your point is almost entirely based on exceptions ("if you have the right console bought at the right moment in the right place with the good controllers, you may able to play the game"). That's a whole different situation from a port of SM3DW on the Switch.
They even removed 3D World stages from Captain Toad to replace them by Odyssey stages, that's says a lot.
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