On the topic of base locations, I always try and choose a city to build it on, so I get a better idea of where the base is. Because I live there, I start with one in Detroit, and my secondary base is typically in Ankara due to radar coverage. I run squads out of both, my remaining six bases turn into Science/Storage bases, and Manufacturing/Storage bases, currently a two science and four manufacturing. Both Primary and Secondary bases have three hangers, each specialist base have two.
Edit: A full release draws ever closer ...