The only one I can recommend is the Best Western on 710 N Old World 3rd Street. I've never had to deal with parking downtown so I have no idea where you could park around there. It was a decent hotel and right by the mall.
In all honesty, the hotel rate is actually really good. My parents stayed at the Hyatt about a month ago and they certainly paid a lot more than the $90 a night that they're asking, and it was the same type of room they stayed in too. It's closer than any other hotel I can think of and closer to more parking areas. Plus with the cold weather we've been having I wouldn't want to do a lot of walking.
Sorry if it sounds like I'm really pushing the hotel but I'm being honest. Since I attend school here in Milwaukee, I know a bit about the area and this does seem like a good idea.