If you'd like to compare the two systems by yourself, here are the schematics:
Unisystem VS schematic
NES CPU, PPU, Memory and cartridge connector.
NES input circuitry (controllers) schematic.

The Unisystem VS arcade motherboard is like two NES on the same board, without cartridges (the roms are on-board).

A few things the NES and Unisystem have in common:

• The same CPU (2A03) is used. (The 2A03 is a modified 6502)
• The PPU is register compatible.
• Same memory map.
• Controller buttons are read the same way.

A few differences:

• The PPU color palette is different. The NES uses a 2c02 PPU. The Unisystem uses other PPUs such as the 2c03, 2c04 and 2c05. All of them have different color palettes. (But I think the 2c02 and 2c03 have similar palettes).
• The arcade PPUs have RGB outputs instead of composite. (RGB is much better!)
• The arcade motherboard has dip switches to configure the game (Number of lives, credits per coin, etc...)
• The unisystem has an input connected to a coin acceptor.
• The two systems on the Unisystem motherboard can communicate together
• The Unisystem does not have a lockout chip.

The NES system architecture is quite flexible. The cartridge can have additional components to allow the use of bigger ROMS or additional memory, depending on the game requirements.

This is not possible on an Unisystem VS since the roms are installed directly on-board. The games must use the ressources available on-board. Here's what's available:

• Program ROM from $8000 to $FFFF. (Identical to the NES)
• Additional memory from $6000 to $7FFF. (Some NES games provide this)
• 2 16Kb ROM for the PPU, Selected by the CPU using a spare output. (Possible on a NES but I dont know any game which does this.)
• There is 4Kb of memory installed for the PPU instead of only 2Kb. (Some NES games provide this too)

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