Thanks for the feedback Admiral, my reasoning for tying the governors to the capitals was two fold. Firstly was to reduce the learning curve as I said, but what I neglected to mention was that it would be nice to add more or a role to the capitals (if they even exist in GC3) rather then just a single planet boost as capitals usually imply governance.
Sorry, Master Chief Petty Officer, I'm afraid I'm not Admiral, just a medium tank. 
I like learning curve idea, but idea of getting governors and/or ministers not from very start is strange.
From learning curve perspective, governers could be introduced after we colonize the very first planet, and ministers could be introduced after we construct first building from their respective area of responsibility. IMHO that only would be logical.
Experienced players, launching single-player freeplay, or multiplayer session probably would prefer having ministers opened from very start, already knowing how they are going to distribute their industry, R&D, or fleet. Probably they will already have templates for governors. If we will have templates. Say: planet, class 17, build this, this, this, and this, then fill with R&D labs/manufactures/be fruitful and multiply.
I love your idea of having separate 'footings' for your empire! That's a fantastic approach to manufacturing and could also be a great diplomatic tool, if your chosen footing was visible to the other races you're in contact with, or perhaps became visible after a level of espionage was reached. It would be excellent for those people who love longer term planning and keeping a finger on other races pulse's!
Fate,
I think footing should be hidden from anyone who doesn't have spies or eyes (satellites/stealth reconnaissance ships) in your space, or who is not your ally/teammate. Should we be allowed to have joined research/manufacture/combats, and combat will no longer occur from big guys to small guys, thus finally allowing us to cover big, but damaged ships with smaller, yet unscathed, that could present theoretically viable solution.
For example, you've been spawned at corner of the map, hence your systems are somewhat better protected, while your teammate was spawned closer to centre. So you can afford slight shifting into R&D, while he has to protect his and yours longer borders, forcing to go into early manufacturing. Using terms I coined, it could be wise for him to pick Conveyor riveter, or even Wartime simplifier, both during expansion and industrialization periods, mostly ignoring R&D and nice development, while you could pick up Conveyor riveter, and then, after initial explansion shift to Perfectionist, and concentrate mostly on R&D. At the end your joined fleets will have his weaker, but massive "cannon fodder" up front, and few of yours "glass cannons" (maybe not so glass) behind. Then you will lend your teammate a hand with tech, allowing him to shorten the gap, and in turn he will lend you all might of his manufacturing.
And then Supersmart Shathi arrive and chew up everything. 
If my approximations are correct, this could work. Of course, I used very rough numbers. What I don't like about my idea is general patternization of this scheme - during expansion/exploration stage you choose Wartime simplifier or Conveyor riveter, simply to build more colony and scout ships, and to construct buildings faster, even at expense of their subsequent reduced performance - quantity has a quality of its own. During settlement stage you replace them with Perfectionist, who will help you with R&D and upgrading older buildings into better new ones. During calm stage you could pick up Logistics genius, who would greatly reduce maintenance cost, thus, "collaterally" improving your economy. During wartime you can go back to one of first guys. In case where we just issuing decrees, we just switch them as we see fit, ot won't changes the point.
To add some variety to that, ministers could have Fallout-like traits and perks, to make them more "human-like" (if we speak Terran Alliance:)). They aren't necessary to have negative features, but they could have some variety between. You can have "crazy botanist" who could make your apple trees to bring you maize, pumpkins, or even beef steaks (no questions asked, I said - he is crazy!) and make them grow anywhere, be that dryest desert, or arctic cap, with temperature close to absolute zero. Give him time and he'll have tree growning out of his head (and he will name it Bob). But give him a gun and he'll use it as support for his plants. Or you could have armament designer genius, who would greatly improve your armament R&D, up to discovering new tech early on, and improving all armament of your ships, regardless of tech discovered. But give him crops and all he could do either turn them to new propellant, or turn them into projectiles - don't expect him to improve your farms productivity. Or your Logistical genius could knew any smallest nut's or bolt's location in your system, but don't show him to foreign ambassadors, because your minister is somewhat unkept and untidy. And smells. A bit. He is so concentrated on his duties, he has no time to take a shower, and he sleeps on his table.
Simply put, I want to see our ministers as human beings, not simple robots. Unless they are robots, but even in this case you could explain that through firmware.