With my Shedd-bashing, I forgot to mention one detail. If you're going during the summer, they usually have Jazzing at the Shedd on Wednesday nights. They open the aquarium late, and have live music. Its the best way to see the Shedd with minimal crowds, and you can see the Navy Pier fireworks from the balconies and walkways. If your going to be there during the week and want to see the aquarium, its the absolute best way to do so.
The walkways near the Shedd are also awesome for photos- you can get beautiful pics with the skyline and Navy Pier as your backdrop. At night, its one of the best places to get pictures of the city all lit up and the Navy Pier ferris wheel.
If you have a membership to a museum or aquarium in your home town, check out their reciprocal list. I know the MSI participates and I believe both the Shedd and Field do as well. I'm not sure if they do free entry or just discounts though. The Lincoln Park Zoo participates in the AZA reciprocal program (Brookfield does not), but since they are free you just get a discount on food/merchandise. Still, any discount is better than nothing.
They don't have the free trolleys anymore, and I hate using the bus system. We do cabs, walking and the water taxis and have a great time. There are also a few companies that do private trolleys and double decker buses, where you pay a flat fee and get hop on service between their different stops all day long. I would not rent a car due to the outrageous parking costs around town. Your much better off using cabs and other forms of transportation. If you don't have your hotel room yet, I would try to get one that is near Grant Park. You'll be fairly close to everything and can easily walk to the lake. I wouldn't swim in the water though
There's also a
Lego store in the same building as the American Girl store, but I believe on the second floor. I think the second level of the AG store has an exit near the Lego store too. Even if your not Lego fans, you should take a few minutes to check out the window displays. They have a pretty cool one with the Chicago skyline made entirely of Legos
I would also avoid the Sears/Willis tower unless you are there on a weekday morning. Even then it gets crowded, and its not uncommon to have to wait an hour or two in line just to get up to the deck. The Hancock building is a less popular alternative, and if your only in town for a few days, the skydeck might not be worth the long waits and crowds.