I was thinking, that since the benefit of a specialization that isn't supported by the structures on the planet has a reduced output, reducing it further might be sufficient to balance it? Maybe?
A 40% output nerf could do it, more or less. This post from a few months back gives a rough outline of the math:
Say both you and the AI have 3 planets, each with 100 production. You give each 900%'s worth of buildings, one specialized on econ, 1 on industry and 1 on research.
The player specializes each planet to use 100% on the correct output type. So you have 1 planet producing 1000 industry, 1 producing 1000 research, and 1 producing 1000 econ.
The AI uses the empire-wide wheel, and set itself to 33% on each. The industry planet produces 330 industry, 33 econ and 33 research; the econ planet produces 330 econ, 33 industry and 33 research; the research planet produces 330 research, 33 industry and 33 econ. It's total production from the 3 worlds combined is 396 manu, 396 econ and 396 research.
If it tries other settings, then the results are not improved. If it goes for 50% manu and 25% elsewhere, we get the industry world on 500 manu, 25 econ and 25 research - a nice increase for industrial output. But the econ world is now producing just 250 econ, 50 manu and 25 research; the research world is only producing 250 research, 50 manu and 25 econ. It's total output is now 600 manufacturing, 300 econ and 300 research. It's still stuck on 1200 output, where the player is pumping out 3000 total output.
Focuses complicate this a little, since they mean the AI player gets, on average, 58% of production * bonuses for their specialised worlds, and 21% of production in the off-focused. Where ever the global wheel sits, this average will be the same, as any increase in one area will cause an equally significant decrease in another. With focuses, the total output will be higher than the above (which was written during 1.2, before offsets existed, and regards why the global-wheel-dependent AI was failing to match the player) but still much lower than the specializing player can manage.
So we repeat the exercise above. 3 planets, 100 production, 900% of specialized buildings.
The specializer's total output is still 3k.
The focus player's output (with global wheel at 33/33/33, to minimize loss) is
econ world: 580 econ, 21 industry, 21 research.
industry world: 580 manu, 21 research, 21 econ
research world: 580 research, 21 manu, 21 econ.
The actual total is 1878, as there's 1% extra you be distributed.
Moving the global wheel around will not change the total, because every increase to manufacturing in a balanced empire will cost it just as much in econ and research combined. 1878 is 62.26% of 3000, so the focus is more or less a 37.8% nerf on output compared to the wheel. That means a 35%-40% raw production nerf to races using the wheel would bring their average output more or less into line with the average output of other races.
The problem is, any focus-using empire with imbalanced colony types (so having 50% manu, 25% research 25% econ and setting the global wheel to favour manu) will permit a higher output than is possible with wheel-races., as would splitting individual planet production across multiple types in ratio to the focuses.
This is why balancing it would be hell; the optimum production strategy with focuses is to split your production on all planets, with minor deviation from a standard layout based on which focus is being used, and setting your global wheel to roughly match the %es of each type of planet in the empire. Doing so, the player can push his production up an awful lot compared to specializing his planets (though not so much as he could if he was able to go 100%).
Consider a focus player with the same planets as above, but all set to manu. He'd naturally set the global wheel to 100% manu, which leads to his output surging up to 3k - equal with the planet wheel guy. With 2 manu worlds and 1 research world, and the global wheel set to 75/0/25 (so with focuses his planets are 100/0/0 and 50/0/50), he'd get 2 worlds producing 1k each, and 1 world producing 550. This is suddenly very much weaker.
Hence, it's not really something that can be simply balanced, if it can be at all; either wheel use is going to be weaker or stronger, and by significant amounts. The wheel user can always have 100% efficiency, but the focus user's efficiency fluctuates wildly around the average.