The Kansas City Zoo has one of the best Africa exhibits of any zoo that I've been to. They arguably have the best chimpanzee exhibit in the world. The new penguin exhibit looks very cool, although it didn't yet have penguins in it when I toured it.
The Sedwick County Zoo in Wichita has underwater hippo viewing and a stellar reputation.
You don't have an easy choice. If you like African animals and penguins though, I would think that Kansas City may be what you want.