There are already dependencies to yii and its parts.
I am not sure what kind of dependencies you mean?
In any case, there should be examplery code for console, web and maybe rest api.
Maybe the web and restapi could be done with a Gii like generator. E.g. you want to add a blog, easy - goto app generator.
One issue you linked is about the user expecting a index.php, well no idea there. I think create-project should make something which usable from start, gives a better feeling specially for first time users. But could also be “yii init” script doing that.
The other issue is about libraries, using vue or vanilla js or angular - those differ drasticaly.
It would be nice if this is in a separate package, and not bundled.
If I make a console app, I dont need it, same for API. And if I want make web app I can use it then.
Vanilla JS should be default. And a external package which can enhance that.
Voting for make it simpler, multiple templates are tedious to mantain, and I dont see any advantage. I had say, make Gii generator for that.