-More unique level themes. The ones used aren't bad but are very "been there, done that" at this point. At the very least, make them feel more unique, like what Mario Maker 2 did with the 3D World theme compared to the other styles. And yes, parallax scrolling could do wonders.
-A better soundtrack. Not gonna lie, the NSMBU soundtrack is kinda uninspired and boring, not to mention that most of it is reused from its two predecessors. Mario's 3D adventures have fantastic soundtracks; take a tip from them!
-Don't fill player slots with generic colored Toads. Toadette's an improvement but is more of an easy mode character in NSMBU DX, so remove that aspect at least.
-Allow the player to carry Yoshis between levels, like World did. NSMBU had Baby Yoshis at least, so that's something.
-Remove time limits, please! Players should be able to explore to their heart's content, without regard to that awful clock in the corner.
-Don't throw players back to the world map when they die. Better yet, more frequent checkpoints could do wonders.
-Full 3D world maps. Mario 3D World and Kirby Star Allies made me fall in love with this concept and I want to see more of it.
-Sub-games! No harm in making little diversions from the main game when players want a little break. Kirby makes sure to include some in every game these days, but Mario is no stranger to this either: just look at Mario 64 DS and New Mario 1!
-I'll end this with a more controversial suggestion, but at least try to put more emphasis on story and original characters in 2D Mario. Most 3D Mario games have just enough of this to add an extra layer of personality, and Kirby's good with this too. Why not give it a try with 2D Mario?