If you have a look at the things that have already been made to allow 3D in GM then you'll notice there is
a lot already.
If you combine all those and add a bit of code for the things that you need for your game specifically then you'll most likely end up with a pretty decent 3D game.
Admittedly, what could be better is ease of use of all that existing functionality and a somewhat better integration into GM's IDE.
I agree with Yal's points on that, though I think quite a few of them could be solved quite easily:
This can be done more or less using local asset packages. Simply define the contents that a package needs to qualify as a valid "3D model asset".
Quite a few model formats seem to be supported already these days. But it would be nice to have some kind of "conversions library" to easily convert between formats internally.
This is being worked on,
in a way
A mapping of layers/groups of models/groups of geometry/... could work equally well, I think.
No need for a 3D mode if you assume a topdown view (with the z axis effectively pointing into the screen).
In-game you can still use any orientation or whatever you'd like. Use euler angles, quaternions, dual quaternions, ...
Simply define a root parent object and define those variables as object variables. Make all objects that need the variables children of that parent object. Modify instance variables in the Room Editor. Provide that project as a clean and ready-to-use template, possibly again as a local asset package (because why not).
I think that's as user-friendly as it can currently get.
I'd like to add to all that proper documentation for people new to using 3D in GameMaker.
And many interfaces, conversions, etc. Proper interfaces between the file formats and the underlying data, between shaders and uniforms, between external software and GM, etc.
So, personally, I'd say there's not really a need for a GameMaker:Studio 3D but rather a need for 3D in GameMaker:Studio.