The Mojo v3 and Papilio Duo both use the exact same FPGA. There is no meaningful difference in their I/O capabilities.
There are some differences in their peripherals, and they almost all point in favor of the Papilio:
The Mojo v3 uses the AVR microcontroller to program the FPGA, as well as for communications with the FPGA. This is a bit strange, and locks you into using Mojo-specific tools for programming. The Papilio has a FT232H for programming and communications; the AVR is separate. This allows you to use more standard tools.
The Papilio has a pretty large (512 or 1024 KB) external SRAM chip. The Mojo v3 has no external memory; you're limited to the 576 Kbit (~64 KB) block ram available on the FPGA. (There is an expansion board available, but it's kind of expensive.)
The Papilio has an Arduino-compatible pinout. The Mojo v3 does its own thing.
The Mojo v3 has a few more LEDs. So there's that, I guess.
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