I'd be fine with many of the smaller birds (parrots, toucans, owls, turacos and other similar such birds) being in the walkthrough exhibit. Having a free-flight bird show would be a way I wouldn't mind flight coming to the game - it could involve both habitat and exhibit birds*, which disappear from their enclosure and appear in the show. As well as the flight component, where the bird's routes are laid down like a invisible track, each species could have its own unique behaviours that make use of some sort of additional items - things like a pond for pelicans, geese, ducks, spoonbills, ibises and cranes, a tree for parrots, hornbills and crowned pigeons to perch on and a rubber snake for secretary birds and roadrunners to attack. Plenty of zoos have some kind of bird show, which could add a lot of educational opportunities and a new side to management in the game.
* Almost all of the habitat birds mentioned on the forums (basically everything bar the gamebirds, swans and shoebill) are used in bird displays at least somewhere.