The current adjacency modifiers (for the main series of buildings) are very 1 dimensional to me, and encourage specialization to an insane degree. The fact that a world of all factories is the most efficient manufacturing planet, to the point of being the only viable strategy, and allowing a single planet/shipyard to 1 tick build pretty much any ship in the game even is just wrong. 

To address these type of issues I recommend that adjacency modifiers be changed to work as follows. 

Factories ... give +1 wealth to adjacent squares

Markets ... give +1 research to adjacent squares

Research ... gives +1 manufacturing to adjacent squares

Real world justification: Factories provide goods for markets to sell, and markets create demand for new goods driving research, and research makes for better more efficient factories producing newer goods.

Game justification: Having the right combination of buildings can give you a powerful planet that is good in research/manufacturing/wealth, and placement of buildings is still important to get the most out of it. You can still specialise to make use of planetary bonuses and resource bonuses, but now the optimum layout wouldn't necessarily be a completely 1-dimensional planet. You would actually still be required to have a balance of buildings, and a wider range of options on the governance sliders would be feasible. This would also inherently create a diminishing return on specialization rather than encouraging specialization as the only strategy, without actually excluding specialization as a viable strategy.

Strangely, some buildings already operate this way, in that influence, tourism, diplomacy, wealth are all complementary, but the same currently cannot be said for research, wealth and manufacturing.