I haven't played the MK games on PC for years now. I said "screw it" and just play my old UMK3 Sega Genesis cart on a Genesis clone console. GamerzTek MiniGen HD, which features both HDMI and composite AV outputs for both LED and CRT TVs.

Hmm
Honestly, I really haven't had any issues to speak up with the setup that I'm using. I bought a Retro-bit Sega Saturn USB controller and its worked pretty well overall for MK1 and MK3. ( I haven't tried MK2 recently ).
For MK3, what I'd HIGHLY recommend is if you're using a controller that prodominantly uses a D-Pad, is to skip the joystick calibration step entirely by pressing escape after opening the game for the first time. For me, it ran flawlessly and I was even able to get all of the way to the end of the game on novice (admittedly I'm not very good at fighters =D ).

I got my old Logitech Rumblepad 2 to work flawlessly in MK1 using the good ol' DosBOX Mapper.

I even got my Logitech Chillstream (basically an X360 controller with Xinput) to work, but I can't get the D-pad controls to do anything, only the sticks work.

I just figured out that if I change the joysticktype=auto from "auto" to "fcs", the D-pad works on the Chillstream, but the Rumblepad doesn't work at all. I'll play around some more. That's because joysticktype=fcs only supports one controller.

I just used Joy2Key and it works perfectly. I can use the Rumblepad's stick/d-pad swapping button and the Joy2Key for the Chillstream and have two gamepads at once. Nice!

Really frustrating, when i try to configure the controls when it wants to to select a button for high punch whatever button i press just quits to the character select screen and i can't get back into the menu screen.
Also my character is always in 'duck' mode ?? i can bock and kick and that's it. even after configuring a button for punching it just blocks and kicks.

Kinda shocking they released this in such a buggy state.