The biggest problem for me on the Kong emulations is the sound. Most of the X-in-1 boards I've played get the gameplay right (although the controls usually suck) but the sound is off. This is because the real PCBs used analog circuitry for many of the sounds (jump, stomp, walk) and it's impossible to really emulate the analog sounds digitally. Oddly enough it's the imperfections in the analog sound that make them stand out, and the digital emulations are too "perfect" so they don't sound the same.
MAME is also dead on as far as gameplay, and the sound has gotten better because they're doing some really cool stuff trying to emulate the analog, but it's still not exactly the same.
If you want DK, DK Jr., and DK 3 all in the same game, the best way to do it (in my opinion) is to put all three original PCBs in your cab and use an edge connector wiring harness to switch between the 3 PCBs. You have to open up the back to swap games, but it's a quick and painless process.
DK II (i.e. D2K), is an add-on to your Donkey Kong PCB. It was made recently and it's not an "official" Nintendo product (although it's an awesome game if you like DK). You can switch between DK and D2K on your DK PCB without messing with the harness. All you do is hit player one and player two at the same time and it switches games.