Many good things to do listed here.
Don't try to go to MSI on the weekend. You will wait in line for the entire day. FWIW, the MSI is about a $15-20 cab ride each way from Shedd. It is pretty far south.
Museums - Stay on the museum campus near Shedd aquarium. You can see Shedd and the Adler Planetarium in an afternoon, they are right next to each other. Include the Field Museum too if you want to take up your morning. All 3 within walking distance of each other. Park in the East Lot for easiest in/out if you are driving.
Navy Pier is good. Get the fried bucket at Bubba Gumps for lunch. Deep fried Lobster is very good. NP is North from the museum campus (about a $5-8 cab ride).
Hugo's Frog Bar for a very tasty and huge steak and afterwards, bar hotties!
