I agree, M+ GUI is a nice and clean frontend. About Emu Loader, isn't this organized enough ?
I know my frontend is not super-mega-ultra easy to use but, if you have a mame.ini already configured, the only thing you really have to do is select a MAME binary in Emulators Setup screen and let Emu Loader build the games list.
I doesn't support "folders" filters anymore like M+ GUI because it already has a complex filtering system. It's also not a "light" application since there are lots of files in its folder tree.
Currently, I'm working hard to simplify things in the frontend. To make it as easy as possible to setup and use. Sadly, over the years, Emu Loader turned into a bloatware application, filled with crap that almost nobody uses, except for a "few" users.