I wonder how difficult it would be to make a small adapter to plug Atari joysticks into SNES controller ports. You could even plug Neogeo style controllers with a similar circuit.
It won't work. SNES/NES have 7 pins, GND, VCC, two output pins (clock, reset), and three input pins (D0, D3, D4). Only pin D0 is used for standard controllers.
Atari have 9 pins, GND, VCC, 5 digital inputs (4 of which can be switched to output mode for multiplexed controllers such as AtariVox or keypad), and two analog paddle inputs.
A 9-pin port from FPGA, assuming bidirectional communication is allowed on all but VCC/GND, could easily be adapted to controller standards with fewer pins which pretty much includes everything else, even USB potentially. The console could use heuristics to determine controller type and configure the inputs accordingly. So users could craft cheap adapters out of controller extension cables to suit any 9-pin standard.
I would likely buy the Mega NT for this reason, even if the jailbreak software for Genesis/Atari exists on the Super NT.
I'm still wondering if the Kevtris cartridge adapters will ever materialize. Super NT may not have enough I/O pins on the SNES bus to support NES/Famicom carts, though the AVS serves this purpose well enough as a more budget friendly alternative to the NT Mini. I think most other 8/16 bit systems should work, including Genesis. The Genesis is certainly less sophisticated than the SNES so the Super NT should support it if a core gets written (though a dedicated Meta NT unit would be ideal).
Homebrew Atari games utilizing melody boards aren't possible through any FPGA core implementation since the ARM inside the melody cart is too sophisticated. So homebrew game carts, or ROMs compatible with Harmony, will still need a cart port to interface the FPGA console. A cartridge adapter for Genesis <-> 2600 would be simple enough to construct for the Mega NT. A bonus 2600 cart port adapter would be ideal, and obviously SMS would work out of the box using a standard adapter. The Mega NT core could detect the presence of SMS cart and optionally enable FM sound via system menu option.