How far do are you willing to venture from Melbourne? Do you need to be within a certain distance? If it's between Ballarat and Bendigo, I would go for Bendigo any day of the week. It's north of the divide so the climate is better than either Ballarat or Melbourne, warmer too. Often south of the range is socked in with Melbourne Cloud™ while the north is completely clear. Plus in Bendigo you can head further north for your dark sky sites and have an even greater likelyhood of clear weather. Bendigo is close in size to Ballarat so in terms of facilities I don't think there is a compelling reason to choose one over the other for that particular reason. What ever Ballarat has, you'll probably find in Bendigo aswell. Both have easy road and rail access to Melbourne.
The BOM's climate data is telling:
Bendigo:
No. of clear days: 109.9
No. of cloudy days: 105.5
Days with rain >0.2mm: 109.3
Days with rain >1mm: 69.7
Average rainfall: 514.4mm
Ballarat:
No. of clear days: 56.5
No. of cloudy days: 146.2
Days with rain >0.2mm: 158.0
Days with rain >1mm: 104.8
Average rainfall: 635.4mm
http://www.bom.gov.au/jsp/ncc/cdio/c...izebutt=normal
http://www.bom.gov.au/climate/averag...1123_All.shtml