If you were to go with Mario Bros for PC, then you should use a File System like Modern Games use, go ahead , but you would have to disassemble the SMB3 Rom to get the game physics correct, to make it stand out you need to implement something that can't be done with the NES.
If you are trying to recreate SMB3 exactly as it is on NES, and to write a whole new engine just to resemble it as on NES , why whats the point?

then just make new levels for SMB3 on the NES rom, the editor already exists, the engine already exists, and so forth.

And about Legal Issues, be careful because any time money becomes part of the equation , legal issues may follow, the game must be free to download and play , and you must not profit financially directly by the project, you can have people donate money , just as long as donating money is not required to actually play the game, because then it is not donation , it is selling a product that you do not own the copyright to.

that is why you may want to stay from making the game specifically for the PC Platform, as with the NES Platform some on the copyrights have long since expired, I know for a fact that it applies to Hardware. Now games , I am not sure. Because with the new Virtual Console , Nintendo is able to make money on selling NES Games that can be played on the Wii.

But if you have the time and the resources to take on such a large project go ahead, just add some stuff that is not in SMB3.

A good Challenge is always a good thing, what would be even better would be to take Link and put him in another side scrolling game, Zelda , Mario Style, you pick up different weapons as you go along fighting goombas with your sword, taking out the Hammer Bros with the Bow and Arrow.

That would be an awesome game for sure.