I go to this restaurant often - it is my favorite mexican food in town. My brother has lived in Harlingen TX for over 30 years, so I have been able to eat Mexican food there and in several places in Mexico along the Texas border. El Maguey is the only place in the KC area that serves food that meets me expectation of 'real' Mexican! the portions are huge, and the cheese dip is the same as what I get when in Texas/Mexico. Their rice in particular is more like Mexican rice that I have in Texas rather than the Spanish rice you usually get in KC. It doesn't rely on peppers for the flavor, it is made with chicken stockand other seasonings and is very flavorful but not hot & spicy.
They do seem to have trouble with the bathroom at this location, they keep it clean, but there seems to be some kind of moisture problem (not from a leak) that keeps the room very humid and that gives the impression that it is less clean. I think that also may be why another reviewer noticed small flies - they love damp areas. My best guess is that the drainage isn't too good and the moist air is coming from a floor drain in the room. I noticed outside that they seem to have drainage problems in the parking lot, so I assume the ground under the place stays pretty damp.
Don't let that keep you from going to this place - the food and friendly people more than make up for the less than great bathroom.