Maria Posada from The Book of Life, is a lover of books, who can also kick butt.
Besides her strength in geometry, Tip from Home also builds Rube Goldberg machines as her security systems (and they work).
Hiccup in How to Train Your Dragon seems like an overthinking klutz of a Viking, but once he befriends Toothless and seriously studies Dragons, he is able to handle the species and use inventions with them in battle that leave his warrior contemporaries agape.
Edna in The Incredibles, a no-nonsense fashion designer who uses all sorts of advanced sciences in designing custom costumes for superheroes.
Blu in Rio becomes this over the course of his journey with Jewel. His skills that he learns as a pet (i.e. opening cages, skateboarding, climbing) would become useful later on. Linda and Tulio also are promoted to this rank.
Outside of Fred and Baymax, the heroes of Big Hero 6 are a bunch of science nerds who use their talents in various fields (Wasabi's laser-generated plasma, Gogo's mag-lev wheels, Honey's chemistry expertise, and Hiro's robotics know-how) to become superheroes. Although Fred could still qualify for this, as he is an English major at his college.
The title characters of Mr. Peabody & Sherman: They are both focused on knowledge, yet they can be quite heroic.
Dr. Jumba Jookiba from Lilo & Stitch is smart enough to create an incredibly powerful genetic experiment, and strong enough to go toe to toe with said experiment in order to obtain amnesty for the crime of creating him. He did better against Stitch than a 20-foot tall whaleman who was an expert in combat.