One thing that's always bugged me about Civ 5 is that the early resources become completely or very nearly useless later on. Coal isn't much use beyond Factories even when you're still in the Industrial era...
The only use for Coal other than Factories is the Ironclad unit, which gets replaced by resourceless destroyers very quickly. But Factories are so absolutely essential that I don't see this as much of a problem.
Iron and Horses become almost useless after a certain point, yes. On the other hand, you've had a long time where they were adding to the yields of their tiles, and will continue to do so. But don't underestimate the local benefits (Circus for horses, Forge for Iron). Even so, I'd long ago suggested adding a few new buildings, one per resource, to get some use out of the excess (Steel Mill, Racetrack, etc.), and I've long considered putting something like that into the Balance mod to go alongside the city growth buildings.
The easier thing to do would be to, as you suggested, make the Circus actually CONSUME a unit of Horses, the Forge consume a unit of Iron, and so on. But that will hardly make a dent in your civ's overall supply. (I've actually got the game doing something similar with the Living Refinery; it requires a local unit of Omnicytes OR Neutronium OR Dilithium, and its benefits depend on which of these can be found locally, but it also costs one unit of each.)
There's just one major headache to keep in mind. Iron and Horses are one thing, but the later resources are all created by various buildings. Once you get Energy Banks, you'll have more Coal and Oil than you know what do to with,
and this was deliberate. Get Fusion Labs and you'll have plenty of Aluminum and Uranium, although it costs Dilithium. Get Quantum Labs and you'll have Neutronium and Dilithium. And Brood Pits give Omnicytes.
So by the later game, you shouldn't have shortages of these resources... except that the future resources each have two buildings which consume their resource. (You've noticed the Fusion Lab; it's the first of the six to do this.) More on this below.
-Ethical Calculus seems to be a bit high up the tech tree, and I'm not sure why it should require Subatomic Alloys. Just a logic issue rather than a gameplay issue, though.
There are four answers here. Pick whichever ones you like.
1> When I added the three "social" techs, I put one in each Era, three tiers apart. There's no way to do that and have them depend directly on each other. I did this because the Digital and Fusion eras already had 15 techs, and putting more than one in any given era would just make them too crowded.
2> I specifically DIDN'T want to follow SMAC's pattern of having these techs be their own little side chain, because doing that means that people will skip the whole lot of them; I wanted things to be more interconnected. That means more back-and-forth between these and the more "technical" techs, which, yes, will lead to some head-scratchers.
3> It's not that Ethical Calculus, as a concept, requires knowledge of subatomic alloys. It's that the Habitation Domes, which EC unlocks, require that knowledge (even though I didn't make them actually consume any neutronium). If you look at older versions, the Hab Domes used to be at Subatomic Alloys before I added EC.
4> While I did a lot of rearranging when I put them in, there was still a bit of inertia, keeping things where they were. For instance, Subatomic Alloys should really be lower on the tree (lower in Y, not in tier), because the bottom of the tree is the more "physical science" part while the top is supposed to be the biological/social side. But the only way to do that would be to move all three Doctrine techs up a little, which'd rearrange a few other things, and I liked the idea of having at least one strategic resource on the upper half. (Also, Neutronium adds happiness, since it's a luxury.)
One simpler possibility would be to just swap the positions of Ethical Calculus and Ecological Engineering. But that'd mean that Ethical Calculus wouldn't actually require Social Psychology unless I changed some other links, and Ecological Economics wouldn't require Eco Engineering.
Bottom line, a lot of the tech connections don't make a lot of sense, but that's actually nothing new. SMAC had the luxury of not needing to make its tech tree look pretty, so they'd have techs connecting to each other from opposite ends of the tree, but I need to have it look at least a little hierarchical.
-I was rather surprised to find all my Dilithium used up when I started building Fusion Labs! The standard-game buildings which use resources say it very clearly in their mouse-over descriptions, I think the new ones need to follow suit.
I can do that. For reference, the buildings that use resources:
- The Fusion Lab and Gravity Shield (both early Fusion Era) both use Dilithium, well before you'll be able to generate it with a Quantum Lab.
- The Centauri Preserve and Nanohospital use Omnicytes, although the Centauri Preserve can only be built if you have a local deposit of them and the Nanohospital comes well after the building that can generate more.
- The Nanoreplicator and Robotic Assembly Plant (both Nanotech Era) both use Neutronium.
- The Living Refinery national wonder uses one unit of each.
The existing interface will tell you if you don't have a resource that one of these buildings needs, and the Civilopedia will list out the resources, but I can add to the tooltip as well.
-Natural Wonder resource output is usually a little anaemic even in the standard game, but by the late-game in the Content mod, they actually become a waste of a square. Is there a way of adding tech-provided Natural Wonder output increases, in the same way as for tile improvements?
No, there isn't, unfortunately. There's a sort of cheat you can do where you place a custom improvement on the wonder's tile, and then improve that, I suppose. (I actually do that with the Monolith improvement: it creates a natural wonder on the same tile as the improvement, and the two coexist and add their bonuses.) But in the core setup, Natural Wonders are basically stuck at their original values.
Now, I've actually been planning on doing something about this. Not the tech yield part, but improving natural wonders in general. I mean really, Old Faithful gives +2 research and nothing else? Where's the income from tourists, or the fact that Yellowstone isn't exactly a desert that contributes nothing else? And really, EVERY natural wonder should provide at least +1 happiness if it's within your borders. (Ideally you'd get the happiness if it was worked, but that's not possible at present.)
-Had another idea for an addition: I love the whole tile improvement... er... improvement... mechanism, and thought it could be taken further. If you make the early Wonders provide a bonus to specific tile improvements in addition to their current stuff, it will provide a kind of non-arbitrary racial trait.
Unfortunately, there's no XML stub that does this. Buildings can improve the yields of various local improved resources (see the Mint or Monastery), but nothing empire-wide and nothing that keys off improvement type directly.
Also, this can be horribly unbalanced. Take the example you gave, of Stonehenge giving +1 gold to mines. That's insanely strong; even if you weren't in particularly hilly terrain, you'd be making more money from that than you would from your trade routes for quite a while. This creates an insurmountable economic advantage to whichever civ happened to build it. I ran into something similar when trying to balance the tech yield improvements; boosting Quarries, Pastures, etc. wasn't too bad, but any boost to Farms, Trading Posts, or Mines had to be handled VERY carefully, because they could cause a drastic shift in balance. (That's why the Farm and Mine boosts were research instead of something like gold.)
So really, you'd want something fractional. +0.25 gold per mine, that sort of thing. The XML can't handle this, but since the XML can't do what you're asking anyway, you'd need to go Lua, and that CAN adjust for fractions. But it wouldn't be easy, because the code isn't set up to handle this sort of mod well, and the UI wouldn't display it correctly.
The related issue is that it's too sensitive to the tech leader. In a lot of games, once someone starts getting some of the Wonders they'll begin to sweep the rest, because they get enough of an advantage to maintain a tech lead and build each wonder before the other civs even unlock it. Doing what you've described makes this worse; one player would get all of the +tile wonders, and end up with an insurmountable advantage. (This is a big part of why so many of my mod's wonders are actually National Wonders. I wanted to make sure that you couldn't just run away with all the good effects by having a tech lead.)
And finally, there's a different problem. If you start in the Industrial Era, for instance, then
you can't build Stonehenge. Wonders have a MaxStartEra entry; if you start a game after a certain point they're removed from the list. So if the game's balance depends on whether or not someone has this Wonder, there'd be problems.
I'm not suggesting removing the tech-based boosts, I think they're fantastic, but this addition could create an extra element to the gameplay.
The biggest problem is that it just becomes too much, after a while. If one worker's tile output is too high, then they'll never want to work a Specialist slot, or vice versa. And if you're adding a bunch of Wonder effects to boost all sorts of tile yields, then you quickly upset that balance. (The same goes for the Policy-based yield improvements, although at least there the only policies that do this improve science only.)
I ran into this often while tweaking the mod in its early days; sometimes you'd have all the specialist slots get filled and no tiles being worked, sometimes you'd have the reverse, and neither is a good outcome. So what I've got now was designed around the idea that resource tiles should ALWAYS be worked, but that non-resource tiles should often be inferior to a specialist slot depending on the city's needs.