1. As you mentioned, specializing works well with capitols. It's also good with revenue planets, because you need a large, happy population with market centers to generate a lot of tax income. For most decent sized worlds, I start with a factory, a starport, then 2-3 more factories followed by whatever I'm specializing that world in. A high PQ world that specializes in manufacturing (i.e., lots of factories and your industrial capitol) is useful to quickly build trade goods and galactic achievements before the other races. Research benefits the least from specialization.
Regarding factory improvements, no, there's no way to get the older but cheaper factories. What I usually do is wait until all or most of my worlds need mfg upgrades, then I focus their social spending AND the global slider for a few weeks until they've upgraded.
