I used whole unprocessed wheat flour once, because Im not supposed to eat white processed flour anymore.
Not what I call a good cupcake. It was edible, but it was also something you might expect from "Ellie Mae Clampett"!!! LOL
I've found a "slight trick" to making cupcakes from other flour sources.............
Don't make cupcakes, make muffins. For some reason a muffin mixture turns out a whole lot better than the standard cupcake mixture. And if you want frosting on it, just slap some on.
I mean, even if you use whole bran flour to make muffins, they will be light and fluffy. But if you use the same whole bran flour to make cupcakes, they turn out like bricks. So, anytime I would use a different kind of flour for making cupcakes, I would make muffins instead and just put frosting on them.
Same way with cookies. If you use a higher grain/unprocessed flour for cookies, they turn out harder and sometimes inedible. But if you make a cake batter from it, and then make cookies from that, they turn out just right.
The one thing about baking is there is LOTS and LOTS of trial and error processes to go through until you find one that works!!!