With toddlers, the Wild Reef is my favorite space for fewer crowds, great animals (sharks!), and exhibits that go to the floor. Underwater viewing is also great, although you may have to look around for the dolphins some, and the nearby penguins are fun. Amazon Rising is a fun exhibit that reaches to the floor, but it gets packed on busy days, so you may decide to skip it if your toddler is not a confident walker (or is too confident/quick and not yet good at staying near you!).
The other Waters of the World exhibits (besides Amazon Rising) exhibits are often higher up, although as they are updated Shedd has done a good job of making them easier to see into. The Caribbean Reef is pretty entertaining, though, and not super high-up.
Across from the penguins is the penguin play area, which is pretty fun for toddlers once they can climb up small stairs and go down slides confidently. You can come in and help, but it's difficult to navigate much once there are a lot of kids. Expect a few school-aged groups to come through the play area a few times; they're typically older and run through the area a lot, so it can get tricky with younger toddlers who are still crawling a lot or have trouble climbing up the stairs and going down the slides quickly. The submarine play area is not as good for smaller kids.
The animal spotlights are decent but tricky. It requires sitting (or, if you're lucky, you may be able to carve out a little space to climb up and down and walk around), and normally not great views (you have to get there in advance for the better views—not worth the tradeoff of sitting an extra 15 minutes in my opinion). Whatever you do, don't go in the front row before the kid is very patient, because Shedd is strict about everyone there remaining seated (there may be penguins or a sea lion coming through). That said, it's can definitely be a hit for kids this age, especially if it's dolphins or you're able to be up close for the others for animals on the walkway.
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