I disagree, I don't think it is fun to be having to calculate all kinds of opportunity costs. I think the RA research bonus should be a reward for sustained good relations, I don't think you should suffer from signing a research agreement now by making future research agreements more expensive.
Keep in mind, in pre-patch TBC, we got this 5% bonus from just a RA for free.
What we are proposing now is to keep that system but add a gold cost.
So relative to pre-patch TBC we are reducing the value of research sharing. So the idea that suddenly we can race ahead and get to Rifling super-early is not realistic. We aren't talking about vanilla research agreements that give (half of) a tech, we're talking about a 5-10% bonus.
I think the gold cost for these research agreements needs to be very low, and needs to scale by era. Otherwise; suppose it costs X, with X~- 200 gold. That is a terrible deal in the early game, but an excellent deal in the late game. I don't think we want it to be the case that getting a research agreement in the early game (which might only be 3-5 beakers per turn) is a waste of gold.
With (2), which is more meaningful: if it takes 25 turns for Civil Service which an RA would lower to 15 turns, or using an RA to shave 1-2 turns off of a Modern era tech which can normally be researched in 5 turns?
You're not considering the fact that the opportunity cost of X gold varies.
You can't just ask which is more meaningful a benefit, you have to also ask which is more meaningful a benefit: cost ratio. The opportunity cost of paying X gold for a research agreement is much higher in the early game, because gold is scarce. In the late game, gold is common.
Also: how is a 5% research bonus going to reduce Civil Service from 25 turns to 15?
The research turn reduction is proportional. If the research agreement reduces a modern era tech by 1-2 turns, then it is probably going to reduce a medieval era tech by 1-2 turns (assuming a roughly constant number of turns per tech throughout the game).
Given that before we had the same mechanism with zero gold cost, and it was arguably too strong but not super-too-strong, I would suggest that the gold cost needs to remain fairly low in the early game. The benefit isn't that large. The research advantage should be a reward for having a DoF, if you sign the DoF then you should nearly always want to take it.
But more to the point; other gold costs retain roughly constant output : cost ratios (a granary costs you X gold whether you buy it on turn 50 or turn 300). Other benefits should also do so.
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By the logic you have, we should make unit and building purchases cost more for each one you buy. Because, you know, it would create more complicated decision-making.
But I hope we can agree that would be not-fun.