What is the best the best will be always a pc joypad,or if you want the arcade fell you could buy an arcade stick it depends on the use for example if you are going to use the joypad on different stuff than you have to check if it works for example the ps4 pad doesnt work with south park stick of truth,doesnt work with one piece pirate warriors 3,dead or alive 5 last round but it work on pcsx and pcsx2 but you can buy an exclusive pc joypad and you will get everything working (with some rare exception the games programed to use xbox360 joypad).
As always the pc joypad will be the best option specially for mugen because is plug and play,with the difference of other stuff for example you need a special program to get the ps3 and ps4 joystick to work so is out of question.