I recently experimented with the military production bonus while starting a new game and I have to say, I rather like it. For 4 ability points, you get a 50% productivity increase. When combined with other bonus buffs, it's now at 80%.
To me, it's starting to seem like a no brainer. I mean, think about it: the game is about cranking out ships and sending them out to build starbases or destroy other ships. Almost all other considerations (economy, diplomacy, morale, research, planet quality, etc) are merely factors toward achieving that goal.
Why tinker with the production factors when you can cut straight to the chase and boost output directly? It seems to me that a 50% military production bonus could be worth more than 4 other bonuses combined.
Plus it's allowing me to more quickly build a respectable military and keep the AI off my back. I'm not saying the other factors aren't important, I'm just saying that I think the military production bonus provides the most bang for the buck when starting a game. Try it.