Its 2 major flaws are being burstable and duration depending on your number of charges. Add to this the fact that you lose every charge at the end, it makes it unpractical in the vast majority of the matches.
They could do a lot of tweaks to make it strong. OD Mugen could be unburstable for the duration of the Mugen, it could regen our charges instead of slowing down the meter, it could do a lot of stuff actually.
With the new combo system based on a timer, doing Mugen with 2 or 4 charges gives you the exact same combo, only the ender (if you have enough ressources) will change. This is... stupid.
Anyway they probably didn't change it at all so whatever, just random ranting here.