With the limit of 1 ship/shipyard/turn and 1 improvement/turn, cost reduction techs quickly become useless - hence I end up going for the "improved performance" techs (since maintenance is trivial).  For engines & sensors, I go with mass reduction - filling a ship with low-end drives + mass reduction bonuses is actually cheaper and more effective than filling the same ship with high-end drives using cost reduction.

Weapons have the only real decision to make - choosing range allows superior forces to wipe enemy fleets sooner, minimizing damage, but choosing mass reduction gives your ships more long term firepower.

Yep, we can easily make planets which can produce one unit per turn, so making that one unit better is the best option by a long shot. Most of these specialization choices are like this. There always seems to be one options which is superior.

There is no such thing as a civilization which is poor at manufacturing. The biggest malus is -25 production. This hurts colony start up and research/economy planets (ironically perhaps). Actual production planets don't even flinch at this penalty.

For ships, I go for more speed and then space. If you want more power, you can always add another weapon.  I also just go for missiles and no defenses. Missiles are a great standoff weapon.  If I have space for a shield or armor, I figure one more missile should fit there.  

Until I can get carriers. Then it's all carriers. 

Doesn't space = speed? More space = more engines which means more speed, right? The choice that comes to mind here is right after Ion engines. Do you take 10% speed, or 20% reduced mass? A player looking to optimize speed here would pick the later option right?

BTW I totally do the no armor, all missiles approach to early ships. I've fitted 7 harpoons on an early military ship, and was just like "Come and get me!" I find it pretty strong so far.

I really hope we see balance improvements soon, more then anything else. This game is all about choices: Race options, tech trees, idealogy, moral decisions, planetary structures. Yet, despite this, I am never actually weighing the choices I face. Their is either a clear winner, or the effects are too insignificant for me to care. (my planet has a -10% research penalty..oh nooo...). I think if I started to care about my choices more I'd be able to get a lot more into the game.