A mapper that allows PRG-RAM can solve both those problems, but you have to make sure you set it up properly at reset time.  You can add the bare essential amount of code required to switch to a free ROM bank with your setup code when the game resets.  The custom reset routine can copy some code to PRG-RAM while also initialising whatever variables you need out of there.  Then when the reset routine is done, you can jump to code in PRG-RAM which restores the original $8000-$FFFF used by SMB1 and start the actual game from there.  To call your hacks from within the game, you can just write JMP $6000+whatever and it will overwrite only 3 bytes, which you can easily account for in your custom routine.

Some mappers also allow ROM to be swapped into $6000-$7FFF but only one that comes to mind is Sunsoft FME-7.

As for actual hacks that expand the ROM with custom hacks, there is this hack that adds a Metroid style environment to it but I can't remember it's name.   Only that the guy who authored it was "ATA".