I've never lived in Indy, but have lived in Milwaukee. I gotta say, my wife and I now live in the Twin Cities and Milwaukee is really the only place we would move back to should it be up to us. We both really loved the area, theres lots to do (especially in the summer), thanks to the lake, the winters are much more bearable than they are here, cost of living is DIRT CHEAP (possibly enough to make up for tuition depending on what your plans are for buying/renting-again I don't know much about Indy). The school districts that surround the campus (Wauwatosa, West Allis, Brookfield etc.) are all very good (plus there are a host of decent (although I disagree with them in general) private high schools), and the area where the school is fairly safe.
The city itself is odd though, probably the most segregated city I've ever been in. There are some rough areas, but you surely can find an affordable home in a nice area.