Do Wildlife Explorers Basecamp and the Reptile House/Walk area first. This area become much more congested the later in the day it gets.
From there, I personally go back across the entrance and start in the Australian Outback and Urban Jungle areas before going down through Africa Rocks. Once I get to the bottom of Africa Rocks, I go through the Panda Canyon and adjacent leopard exhibits before doing a slight detour to the Ituri Forest and the lower waterfowl ponds. I then go up Eagle Canyon, around the remnants of Horn and Hoof Mesa, through Polar Bear Plunge, and on to Elephant Odyssey. Upon exiting Elephant Odyssey, I go through the Kopje area and then back to the Koalifornia Boardwalk to go down Bear Canyon and Sun Bear Forest. From there, I'll go up the stairs above the tufted deer yards to the lower level of the Owens Aviary, crossing through Owens to Fern Canyon. I'll then go up Fern Canyon and hang a right to go past the orangutans/siamangs. From there, it is through the Parker Aviary to then go down and go through the other levels of the Owens Aviary and back up through the Aviary Trail. After completing Aviary Trail, I hang a right, go around the gorilla exhibit and then up through Hippo Trail before going down and through the Scripps Aviary. From there, I go down past the bonobos, mangabeys, and crowned eagle, make a U-turn, and then go back to go all the way down to Tiger Trail. Then you can take Tiger Trail all the way up to Monkey Trails and Forest Tales and explore the multiple level viewing of the primate and babirusa habitats at your leisure before heading out past the flamingo lagoon. I always finish with a quick jaunt over to the aviary at the bus loading station and then call it a day!