A SNES flash cart would be great. It would be good to make it shaped like the Game Genie or Pro Action Replay, so that a DSP1 cart could be attached ontop for compatibility with DSP1 games (Super Mario Kart, Pilot Wings, etc). The passthru could also be used for the lockout chip, as well as for backing up your own carts to SD cards. I think that it would also be a good idea to load games off of SD cards, so that large amounts of games can be stored on the cart at the same time. This would also remove the need for a separate USB programmer device.
The SNES flash cart should have 96Mb of RAM, 1Mb of NV-SRAM, and a real-time clock, so that it can run any game that can be run on any other SNES copier or flash cart and more! It would also be more user friendly, as every SNES game can be stored on a single SD flash card. Real-time save and cheat code support wouldn't be necessary, as the SNES flash cart could be used with a separate real-time saver or cheat code device, since the SNES flash cart is no larger than a Game Genie.