Well...I'd pretty much just pick some spots you want to see, and then see what's along the way.
We were there yesterday. DS wanted to see the pandas first off. Well, the pandas are tucked away, so we first went along the Orangutan (or as the zoo in Seattle calls them, Oran Utan) path, saw some piglets nursing, then found the Tiger trail. Had great timing, as we came up to the tigers just as the zoo guy was getting ready to feed them. After that, continued along, saw whatever there was, saw SO many animals (I personally adore the habitat where they have otters and some sort of monkey, it looks so fun for them!), and finally found the pandas. Saw the 9 month old panda frolicking, had almost no one behind us at first and took 1000 pictures (not usually allowed on the closer path), then finally had to move along (go to the top path, hug the wall, so you're not stopping the line) and took a few more pix.
Stopped near the red panda across the way, had a lunch we brought in (totally allowed), reviewed the map and plans.
The normal tickets now allow full use of the bus, the skyfari thing, and, hmm, something else. Take advantage of it! We never caught the bus, as it was always going the way we were not, but we did use the skyfari thing. We actually walked to the front of the park to catch it up to the top of the park so we could see the Polar Bear exhibit, and of course the things on the way between where you get off of the sky thing and get to the polar bears.
After that first DS wanted to see the big cats, but that changed to elephants at some point...the elephants are just beyond the lions and a jaguar, so that worked. (the other big cats (besides what I've already mentioned) are along this one path that is kind of out of the way...we ended up missing that entirely this time, and last time we were there it was at the end of the day)
Just kept picking the big things to see, and saw almost everything else as we went.
They have big people movers to get you up some hills if you'd like; a combo between escalators and the people movers at airports. Since DS wasn't in a stroller, that worked well for us (one goes "through" or past the dingo, which we just barely saw as we passed it).
We didn't plan to buy food, having packed it all in, but DS is eating every couple hours right now, and required food at around 3, just after we saw the elephants, so he ate at the restaurant there. Expensive, but hit the spot for him...bought a fruit plate/box thing and a kids meal with decent mac and cheese, and he got some good food AND a plastic bucket AND plastic cup with lid and straw. Also got out of the direct sun and had another chance to look at the map.
So that's basically how we spent our day, and it was a good one! Have FUN! Wear hats! I kept reapplying sunscreen to myself and ended up burned....everyone else had hats, didn't get as much sunscreen, and none of them got burned at all. Harumph.