Something to think about when you buy an arcade game is what you actually want out of it....are you in it just to play a single game? 60 games? 3000+ games? There's an option out there for everybody. Take me for example, when I bought my first machine (Simpsons 4 player), I wanted an original cabinet, with full side artwork, and a bright monitor. I paid more to have an original Simpsons cab. I probably could've gotten the game for less, but it might have been in a cabinet that was painted black, no artwork etc. For my collection, originality is important. The only time I've ever gone not original was in restoring my Millipede cabinet. We were having issues with the original pcb, so for less than the price of a replacement, we bought a 60-in-1 board that contained Millipede, Centipede, Breakout, Arkanoid and a few others that can be operated with a trackball. It also contains Pac-man, Donkey Kong etc, but I turned those off because I din't want to install a joystick. Millipede was never a favorite of mine, I just got the cabinet fairly cheap and wanted a project to occupy some time, so that was it. So I say all that to say this: for me, original components are key, and that usually translates to more money. I'm okay with that, in most cases.
As far as the value on the machines you're looking at, there's other factors at work. Even though the cabinet design is THE EXACT SAME on a MK machine and a Killer Instinct machine, the Killer Instinct machine will bring more money if someone wants an original cab. You can expect to see that machine to sell between $800 and $1200, where an MK2 will sell between $250 and $600. There's certainly exceptions to those rules, but those are pretty good ballpark figures. That's assuming they have good monitors, all controls work, etc.
If you have any questions feel free to throw me a message, and I can give you my opinion on what you're looking at. Also remember this, you WILL have maintenance along the life of owning a cabinet. Monitors go bad, boards fry, power supplies go out, so just be ready to pay for that. Let us know what you get, it's always great to see more people get into the arcade hobby. Cheers.