Not that it matters, but I asked the same Chicago zoo/aquarium recommendation-question prepping for a summer 2013 trip back in February. I'm currently sitting in a Chicago hotel having been able to successfully do Brookfield, Shedd, and Lincoln Park on three consecutive days. Since Moebelle's posting was more-current, I'm taking the liberty of piggy-backing her notes to toss in my two-cents...
Brookfield - my wife and I had our six year-old and three year-old in tow, but they have above-average attention spans and we're used to cavorting around larger-sized zoos. That said, despite arriving near opening and staying until closing time, I admit we ran out of time and maybe missed, perhaps, one-third of the park. Despite the hype from a few friends, I was underwhelmed with Tropic World; so much space dedicated to so few species, hard to see, and I'm shocked some LCD-parent hasn't "lost" a child over a railing or somebody hasn't tumbled down the gorilla "stairs." The dolphins were closed, due to the calf birth. We had to rush, but I loved the newer Great Bear Wilderness. The pachyderm building interior was a blast from the past, and having the kids, we were sucked into their 'Dinosaurs Alive' exhibition... now making my 'robot dinosaur count' at five parks, having now seen them at Cleveland, Columbus, Brookfield, Good and Cedar Point all in the same summer. Egads. Still, I enjoyed the park, despite some of its dated paddocks and would love to go back to see what we missed/take a better look at what we 'ran' through at day's end.
Shedd - for whatever reason, even being a serious zoo/aquarium groupie, I walked into Shedd expecting something more-dated and walked out immensely impressed. I loved the architecture, Amazon Rising, Wild Reef and the Beluga Trail. While we did catch the Oceanarium show, we passed on the 4-D show. Swelling crowds and a cranky three year-old made our final two galleries more of a rapid walk-thru, but I was extremely happy with the visit and would now have to debate myself as to whether Shedd or the National Aquarium in Baltimore would be my fave. (Current edge: Chicago.)
Lincoln Park - Again, feedback had me walk into LPZ with slightly-lower expectations, but I really liked this park. As a "zoo historian," I enjoyed the seeing how the past was threaded into today, such as the interior in the lion/tiger house and outside of several other buildings on campus. The Regenstein Great Ape Center might be my favorite gorilla enclosure I've seen in a zoo. The interior of African Journey, small animal, and reptile buildings were surprising pleasant. I felt the bird building was very 'bleh' and while the wolf and bear exhibits adjacent to the Children's area were lush, animals were difficult to see. I wasn't aware that the penguin/puffin building had closed, but it made me sad, as I anxiously awaited to see the innards of the facility from the old documentary "Arctic Window" I fondly remembered from years ago. Due to traffic and some other circumstances, we arrived about two hours late and stayed until close, and now wished we had had the extra two hours to browse.
While not expecting to hit all three, amazingly, we were able to and am thrilled we did. In addition, most of our first day was spent at the Field Museum, which I may add, I may have enjoyed more than the Smithsonian (and could've spent a few more hours there, as well). Hopefully, all the walking helped us to burn off a few calories from the pair of deep dish pizzas we sampled during the week! Good times!