As I get the feeling some would like to go ahead and get this proposal in I want to voice my opinions/concerns too:
First of all, I completely agree with Mat that this will introduce such a major change in dynamics that we should not merge anything into master now. I'm very much in favor of sticking with the plan to concentrate on the Fighter/Carrier mechanic for this release cycle, and leave other major things for later. Smaller additions/improvements, and fixes of all kind are of course perfectly fine, but Geoffs reasoning why we should not try to do Fighter/Carrier and Influence within this release cycle has been very sound, and should apply to proposals like this too.
So, while discussing ideas is of course very welcome, I strongly propose to postpone anything beyond that for later, at least until we implement Influence (for the reasons Mat cited).
Now to the proposals. We're actually dealing with two different ideas, in this post I want to deal with Geoffs idea, which started this discussion.
The idea to have boni which aren't just flat (like NAI and AA) or purely pop-dependent (as the vast majority), but kind of something in between sounds interesting and has a certain appeal, BUT: I definitely share Mats sentiment that this should not be applied to all or even most of the pop-dependent boni, for exactly the reasons he cited. As an extension to the currently two kinds of boni (flat and purely pop-dependent), yes, as a replacement for the purely pop-dependent boni (or, for that matter, the flat boni), no.
My main objection is, while I've always been in favor of giving more importance/value to small planets and trying to avoid mechanics that make the larger planets too advantageous, this will take things too far. I mean, what's the point in trying to get large and huge planets, and increasing the max pop of your colonies beyond a certain point, when doing that doesn't earn you sufficient benefits? And just keeping some non-capped pop-dependent boni so it's not completely pointless to increase your pop is not sufficient IMO, given how extensive our tech tree in the growth department is, in addition to that the growth specials, etc.
It reminds me a bit of the old mining/industry mechanic of ancient times. Originally, to get PP you needed two resources: minerals (which you got by switching a colony to the mining focus), and industry, which took the minerals and converted them into PP. Which meant you basically had to try to balance mining output against industrial capacity, as an imbalance always meant a loss of efficiency. If your mining output was below your industrial capacity, the surplus industrial capacity was wasted, if your mining output was above industrial capacity, the surplus in minerals was wasted. Which resulted in some micromanagement to keep these two matched, which finally had been deemed a mechanic not fun enough to warrant the micromanagement involved, and therefore mining had been removed.
Basically, what you had were two separate caps you needed to juggle, without really offering sufficiently interesting choices for the player. Applying a cap to all/most of the pop-dependent boni introduces something similar. You have two caps - the pop itself of course, and the cap up to which a certain bonus increases with pop. Increasing your pop beyond what most of your boni can increase to is a waste of investment, as is increasing the caps of your boni beyond the pop levels of most of your colonies (by whatever means). You need to keep them roughly in sync, everything else would mean playing a sub-optimal game.
And for what? Because if the purpose is to limit resource output, this can be done just as well by reducing the boni to pop we currently have. Or making it more difficult to achieve higher pops. I don't see the point of introducing what basically amounts to having several caps which do the same for the same thing.
However, if the purpose is to add another kind of bonus, to give us means e.g. to more fine-grained balancing of high and low pop planets, then I can see the appeal. Where flat boni make pop levels completely irrelevant, and purely pop-dependent boni make pop levels all that matters, capped pop-based boni give some importance to pop, but not so much as the purely pop-based ones. The way I see how this can work is: flat boni are very low compared to the other two (maybe 1 or 2 for easy to get, and maybe 3-5 for those harder to get), purely pop-based give a low bonus per pop, but enough to substantially exceed the flat ones already at medium pop levels, and capped pop-based boni could give higher per pop, but low enough so that the purely pop-based ones are still substantially higher at high pop levels.
Then balance things so that high pop planets offer still sufficient benefits over low pop ones that it's worth fighting over them because of their supreme value, and improving them is worthwhile, satisfying and fun, while making low pop planets valuable enough so that acquiring them is worth considering. The "tall" vs. "wide" empire dynamic idea LGM-Doyle pointed out should be achievable by that, although I think to really get that working we need to introduce the "tech cost increase" mechanic dicussed elsewhere (basically apply the current the more ships you have the more expensive new ones get to techs: each tech you have researched increases the cost for researching new techs). Because that can make following certain research paths more efficient than trying to cover everything. Meaning you have to decide e.g. if you want to go for the techs that make it more ease for you to build a tall or a wide empire.
ALl that said, I'm not fully convinced that capped pop-based boni are needed to achieve this kind of balance. Maybe flat and purely pop-based boni are already sufficient to do all that, balancing high vs. low pop planets, and allow for "tall" vs. "wide" empire approaches. In that case capped pop-based boni would add complexity without adding anything that isn't already there/possible.