We visit Milwaukee every couple of years. In 2009 I did a 64 mile circle ride on a Saturday in early August using the Oak Leaf Trail on the eastside starting in Whitefish Bay and going down to South Milwaukee. Then over Drexel to Franklin where I got back on the trail on the westside up to Wauwatosa where I took city streets over the northern stretch to River Hills where I got back on the Oak Leaf back down to Whitefish Bay. I really enjoyed the eastside bit, but found the trail markings difficult to follow in parts of the westside and there is no trail connection between east and west at the north and south ends. I didn't run into any problem areas on my ride, but hopefully someone local can give you better guidance.

Another good trail to ride there is the Ozaukee Interurban Trail heading north from Brown Deer Rd and going up to Port Washington (and beyond, but it's more boring up there). I did another 64 miles out and back on that the next day (Sunday).