How many people work at NST currently.
Could they do a full sequel to F-Zero GX
They could remaster F-Zero GX or make a spiritual successor maybe? I probably see them more making an F-Zero X99 or Puzzle League 99 next. Oh, but anything using online would still be heavy Nintendo on programmers (Nintendo PTD and Nintendo Services) handling the network/server aspect.
or Mario Maker 2 on their own?
Mario Maker 2 was still way too successful and relevant for a sequel not be an EPD creative lead project. Their involvement would be subordinate most likely. Again, anything online heavy is automatically going to have Nintendo development involvement on the network/server side (look at F-Zero 99).