I think the game start using a 720p ratio. Any levels at their normal size levels could have a border around it (I.e. SMB2 character select).
Plus I think that every graphic, collision, game window, etc. should be at its original size (1x1) to prevent having to resize to just have it not be 1x1, then you'll be able to resize the graphics based on the level window. Basically, make it so that people don't have to resize graphics by 200%. This would help a lot and definitely would get a lot of people to stop complaining about 1x1 pixels on graphics, because they'll be 1x1 in the first place!