1. I'd like to see more building kits/themes, and maybe some extra "pieces" that give us a bit more flexibility in terms of shape and size of buildings, roofs and so on.
2. Also, more decorating items and bits and pieces that make it easier to build smaller props for our zoos. People get really creative with that outdoor switch, which is the smallest colorable "rectangles" in the game, but if there were an array of tiny shapes available, players could design even cooler props and pictures and so on.
3. More vegetation, including a wider variety of flowers that are red, blue, yellow, and orange (we have a lot of pink, white, and purple right now).
4. Some diverse starting terrain set ups that can be used for franchise zoos.
5. A greater variety of concessions and gift shops. Would be great to see Chinese food, Indian food, even some more sit down restaurant type options.
6. Barriers of some kind that prevent guests from walking right through fountains and other landscape items and decorations that extend into a path area.
7. Really small letters for designing smaller signs or adding text to smaller props would be cool too.
8. Working elevators that serve multi level structures? I honestly don't know if this would be easy to fit into the existing game engine, though.
I like darthquell's suggestion of in-between sized cages too. I've mentioned how it would be nice to have more variety of exhibit "vivarium" sizes and shapes, so an anaconda wouldn't be in the same sized vivarium as a tarantula, but many zoos have small mammals and other critters that can be in outdoor enclosures that need to be covered over to protect them.
I'd also like to see guests so actively seek out certain popular habitats and exhibits more assertively, rather than following a path of least resistance and congregating in the entry area of the zoo and "under visiting" cooler exhibits and enclosures further away in a larger zoo. I know real-life people can be lazy about walking too (and not everyone has an easy time walking long distances), but when I visit a zoo, I"m not going to skip seeing the cheetahs or another favorite animal because I have to walk a ways to see it, especially if there's a ride to make it easier to get there.