Both locations of Los Gemelos are great, the one on Odana is a lot more authentic in atmosphere, but they share the strength of great food.
This is the type of place to go if you want no frills Mexican food at a low price. If you're looking for an American-style restaurant and more streamlined food this is not the spot. I personally love the more authentic venues like Los Gemelos because the food tastes amazing, the staff is friendly, and the atmosphere feels as if you are in Mexico.
I really like the gorditas, tortas, and tacos, but honestly anything on the menu is pretty good. The downtown location has ridiculously good chimichangas and the staff seemed slightly more attentive but that could have just been on the particular days I went in. The Odana Rd location has a unique grocery store and usually futbol on TV, so that in my opinion is enough to recommend it first if you're deciding between the two.
I'd say they are pretty much on par with Taqueria Guadalajara, but that restaurant still gets my vote for #1 Mexican restaurant in Madison. Regardless, Gemelos is great and absolutely worth a visit.