To start, MUGEN is great because of it's flexibility and customisation, but it is also great for a couple of other things.

First of all, balance; who hasn't ever complained about the overpoweredness of a character in a fighting game back in the day? Everyone who has complained probably wishes they could balance the game, and this is made possible with MUGEN! You can insert the character you want to nerf, nerf them by tweaking their code a little, and test until the right balance is found. Pretty cool, but there's more.

Personally, I use MUGEN because it is literally the stuff of dreams; seeing characters like Terry and Ryu (my 2v2 team) fight all of these characters from all these different universes for me personally is one of the best things I have ever seen. Where else would you be able to pit Iori against Spider-Man, or Solid Snake against Hibiki?

I guess there's a couple more reasons too, but these are the main ones I think of.