I think speed is overrated. You can start with Ion Engines, which will give you a speed 4 colony ship right out of the gate, and Impulse Drive is just round the corner, which will get you up to speed 7. What's 1 or 2 more on top of that?
Economy is a favorite of mine, simply because there aren't many other ways to boost it. And money makes the galaxy go round...
Diplomacy, morale, influence, bah! Those are for the weak
Soldiering isn't a popular pick, but quite useful IMO - There aren't too many boosts for soldiering either, and an early bonus can make a big difference in the early invasions.
Military production is a double-edged sword. The majority of my games, I end up with a world with a substantial +Starship bonus, and that becomes my fleet shipyard. I surround it with Econ starbases and it churns out almost all of my warships. A military production boost is kinda wasted then - all my other worlds are churning out transports and constructors, so I rarely have a shortage.
Planet Quality... meh. It was a must-have in GC1, but it just doesn't do enough anymore in GC2 to be worth the points, I find.
Another "low-profile" pick I like is Ship Hitpoints. Another thing that can't be improved on in-game readily, but at the end of the day, the fleet that has HP left wins. More HP = GUUUD.
In the end though, what you pick doesn't matter a whole lot. What matters is playing to the strengths of the picks you made.