Edit: not that things can't be made clearer, but can you elaborate on what you are looking for
I'm looking for:
1) Notation that differentiates bonuses applied to one object (ship/ starbase/ planet) vs. bonuses applied to an entire civilization.
I PLAYED 150 HOURS of GC3 before building an Entertainment Capital because I had no way of knowing that the +25% moral bonus was applied to my civilization and not the planet.
2) Clarity in defining what abilities adjacency bonuses potentiate. Hives and Durtanium refineries both give +4 raw production, yet Hives get +% bonuses to raw production from adjacency while the refineries get +% to manufacturing. The Molecular Fabricator and Industrial Replicator give manufacturing, research, and population bonuses but only it's manufacturing benefits form adjacencies and only from manufacturing adjacencies. Not true of the Social Matrix which gives manufacturing and research bonuses and receives adjacency bonuses to both from BOTH manufacturing and research adjacencies. The Krynn Consulate and Temples also gain adjacencyonuses to both influence and moral from both influence and approval bonuses. Do Slave Pits follow either pattern? No. They give bonuses to manufacturing, research, and food, give adjacency bonuses to manufacturing, research, and wealth, and receive adjacency bonuses to their manufacturing, research, and food production from both manufacturing and research adjacencies, but not from population adjacencies.
All of this incoherence in implementation is not provided in the descriptions and must be discovered through trial-and-error experiment. I'm inclined to believe that this hodgepodge is the result of a bunch of legacy code that was never followed up to provide a consistent pattern. A good pattern would be adjacencies potentiating the respective bonuses and only the respective bonuses in ALL circumstances.
3) Bonuses are listed with little colored icons. That could make information so clear. The mind naturaly wants to assume that there is a pattern and a purpose to these to help make the information clear. Research is always blue, tourism is always purple. Easy. Wealth is always yellow. Wait... why is social manufacturing also yellow? And if population is green, and it always is, how does making moral, resistance, soldiering and logistics are green as well clarify the information delivered?
I have misplaced buildings making erroneous assumptions based on the color of the bonus's icon. Without experiment there is no way to know that the Garrison's +20% bonus to military manufacturing (red) gains adjacency bonuses from manufacturing (orange) bonuses, not military.
1) and 3) are easy to fix. If the bonus is civilization-wide, add a star to or after the icon, or wrap it in a gold border. Then change the icon colors for bonuses to be consistent across adjacency groups.
ex:
Orange- manufacturing, manufacturing cost, raw production, social manufacturing, military manufacturing (unless it's intended to gain from military adjacencies instead in which case leave it red)
Blue- research
Red- planetary defense, resistance, soldiering / (capacity, logistics, ship range? or would establishing a separate color such as Steel Grey for ship stats be preferred)
Pink- approval (because it needs it's own color to make the scheme consistent)
etc.
Further clarity could come from coloring the maintenance icon with the type of improvement both in the improvement's tooltip and in tech descriptions where -% maintenance appears so often. If Sustainable Research says -10% maintenance with a blue maintenance icon and my research improvements all have blue icons for their maintenance then I can easily make the association and so could future players instead of having to make an embarrassing "Please! What does this mean?" post asking someone to explain it to them.
