I stayed in 2 places in Bologna, one good and one not so.
The good one, and really, for what we did we should have stayed there the whole time, was the Mercure across the street from the station. We looked out fro a tiny balcony on a little park which glistened in the moonlight on the snow, had very good buffet breakfast, and was 2 minutes from both the station and the last/first stop for the airport buses.
The other was midway between there and the two towers. I won't name it because I know it has better rooms and others have enjoyed staying at such a cute place. Just believe a listing if it says it either has no windows or the window (in our case a horizontal Velux) provides a view of the stars.
We used Bologna to bookend a week in Roma, and made nearly daily train trips to various surrounding towns and cities. It was easy for us to walk through the University and along the arcaded streets to the centre (a bit more hassle if you have a kiddie wink with you) and the buses were very little help because most of the centre is one way so finding the stops ad making use of the short distances (now longer because of the one ways) was not productive..
For us returning to the Mercure for the second half would have made much more sense.