I’ve spent half my life midway between the two cities, and the second half in one of the cities, and I still haven’t come close to seeing everything. So, you get the idea that one must balance the ideal with the realistic. A week and a half (ish) would allow you to see most of the highlights without pushing too much.
This trip presumes arrival by car from the south via Chicago, the way most travelers arrive.
Try to start on a weekend, when more stuff is going on. On your way up from the Windy City, drive along the Lake Michigan coast along WI 32 and enjoy the picturesque vistas of downtown Kenosha and pick up some Danish kringle in Racine for some great roadfood.
(Alternatively, head northwest out of Chicago and visit the Lake Geneva area and, possibly, Old World Wisconsin before cruising into the Beer City.)
Start off Friday evening with a dinner of German food and then retire (you’ll need to, given the food’s, er, density). Feel your soul recharge as the sunrise illuminates your walk to the winged Santiago Calatrava addition to the Milwaukee Art Museum . After a stroll/bike/drive north along the grand lakefront  to the museums overlooking the north end atop the bluff line, it’s time for lunch in the funky Brady Street area . In the afternoon, try to wander the Riverwalk  before a dinner at one of Milwaukee’s legendary fish fries .
Try to hit any outlying site—a tour of Miller Brewing  or the new Harley-Davidson Museum  (or, for the nature/recreation-minded, a visit to the Schlitz Audubon Center ) before returning downtown for a wander through the immense Milwaukee Public Museum .
Pick one of the following. Strike northward for postcard-perfect Cedarburg  or continue a bit farther to Port Washington . Alternatively, head northwest to Holy Hill and, later, Horicon Marsh and overnight.
On day four, from wherever you are, make your way to Watertown and start the Highway 26 History Route (not an official name—just what I think it is) south to Fort Atkinson. From here it’s a lovely drive along US 12 to Madison , where you simply must see your first sunset at the UW Memorial Union Terrace  with a beer before or after dinner.
Start with a stroll at sunrise along the John Nolen recreation path along Lake Monona (you may want to bike this later!). Wander through the nothing-else-like-it Monona Terrace Convention Center. Take in the gargantuan, stately Wisconsin State Capitol . Grab lunch at a food cart and hang alfresco with the Capitol crowd. Start trekking the Museum Mile , which will definitely fill out the first day’s activities.
Arise the next morning and grab coffee and a scone at the University of Wisconsin ’s Memorial Union. Stroll along the gorgeous lakefront path to Picnic Point. Backtracking via the campus, this author would later stop at Babcock Hall  for some famed ice cream! Now, sack out on Bascom Hill with the class skippers. After lunch, visit the grand Olbrich Gardens.
If you’re a type-T personality, on day two, you could alternatively give your feet a break along the greatest city bike trail in the state (no argument here, please). From Monona Terrace  ride counterclockwise along Lake Monona all the way to the Capital City Trail. Continue on this trail through splendid, bucolic countryside all the way to bike-friendly Seminole Highway. Turn right and keep riding to the magnificent UW Arboretum  and stretch the legs on some trails or take a nap under the blossoms. From here, turn left at the other end of the arboretum to the fun Vilas Zoo . From here, you’re just a hop up to the student district.
Either spend a day on the Dane County daytrips detailed within the pages and then overnight one more night in Madison  or hit the Trollway to Mt. Horeb and see what the mustard is going on before driving south to New Glarus and doing some yodeling. (If you’re a road warrior you’ll have time for a limburger-onion sandwich farther south in Cheesetown, a.k.a. Monroe.)
Head west for Mineral Point and find out what the deal with “Badger” is (hint: it ain’t the animal and an aside: all county—not state roads leading to Mineral Point are gorgeous). You’ll need a full day of history-learnin’ and shoppin’, trust me.
Choose one of the following: a full day of Frank Lloyd Wright touring in Spring Green or a full day freaking out at the insanely fun House on the Rock nearby. (Trust me—doing both would be sensory overload.)
Spend the day following the Wisconsin River, along the way watch for eagles in Sauk Prairie, visit many of the unique natural sights in the area, such as Blue River Sand Barrens, Avoca Prairie, Devil’s Elbow, or catch a glimpse of the Baraboo Range from Ferry Bluff.