With toddlers, I really like spaces that they can both see fun big animals, and they have a little more ability to walk/run/climb without crushing crowds all around. Dolphin underwater viewing is a great area with fun animals, and space to move around without too many people usually; the handful of steps by the viewing area always make me nervous, but are a big hit with young kids, and a good place to practice going up and down steps without too far to fall. I love the goats and birds area at Wild Encounters, although some toddlers may not like being up close to goats which are a little bigger than many dogs (they are pigmy goats, so not as big as 'normal' goats).
The Play Zoo is always wonderful to have lots of space to move around and play, while Hoofed Animals (with zebras), Habitat Africa with giraffes, the Great Bear Wilderness, and Big Cats all offer great animals that will be popular with toddlers, and at least some space for the toddler to walk around independently (of those options, Big Cats has the worst space for walking, but the leopards around one end and snow leopards around the other have at least some space). The Birds and Reptiles building is a hidden enjoyable area: several exhibits at a toddler's level, lots of space to walk around with relatively few visitors, and even an open flight area with large beautiful birds.
If the zoo isn't very busy, I love Tropic World with the primates (avoid the space on busy days, though: it's not only hard to see much but you won't be able to set the toddler down much because walkways are narrow and get jammed full of people).
If you're getting food at the zoo, my kids have been regular fans of the pizza at BZ Red Hots. At both main restaurants (BZ Red Hots and Cafe del Sol), you can order your food and then sit while it's being prepared, and walk back to pick it up once the buzzer buzzes. Those two restaurants are the only places with highchairs available.
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