There are two different sentiments that are being conflated here, sometimes intentionally, in order to lend an opinion the force of fact:
1. I don't like this feature.
2. This feature is bad design.
One is not the other. When you say "This is bad design," that's an expression of the latter. It's NOT just that you don't like it. It implies that, independently of whether you actually like that part or not, it wasn't implemented as well as it could.
For instance, I agree with Galgus that some of the resource-specific improvements fall by the wayside. I don't agree that this is necessarily bad design, because of the factors behind it. It does mean that the result is a uniformly Biowell'd everything in mid-game just because. That needs to be looked into. But it's not as simple a thing as resource improvements having to be better - that leads to Civ IV resource-hunting syndrome.
In fact, you could already sort of do that in Rising Tide. Certain agreements boost Strategics by as much as three Culture, Science, Production, Energy, or Health per unit.
Ryika:
That's all good and nice, but there is no "wild, unbalanced idea" here. There's a mechanic that was fun in previous games and it's missing without much of a replacement. Or are you saying that: "Oey, I have an idea! Let's make terrain not mean anything!" is an interesting idea? I hope not.
I don't have a problem with being able to expand everywhere (in fact I welcome that change a lot), but if every expansion spot feels the same, then that just makes the whole system very bland. I mean it would be very easy to change that: Make Non-Strategic Resources somewhat localized, then add big, synergistic buildings to a few leaf techs - and there you go, the very basics of a system where you can still expand but will get rewarded for choosing good spots are in place.
Funnily enough I WANT unbalanced City positions, not the "everything is on the same level"-system we have now.
Hm. Acken's turn vic notwithstanding, I think he overstates the sameness of the terrain by a pretty large amount. You do kind of have to get out there and settle land, and settling land at all is more important than settling fantastically good land; but they're not all the same.
Otherwise, we wouldn't differentiate between starts at all, and we do. In particular, having Titanium is a pretty huge leg up over not. It's a fairly dramatic difference. You should easily go for the Titanium sites if you have a choice.
In addition, being on coast allows you to make naval units, and being on water changes your city's nature fairly importantly - all also not the same things.
There's already systems in play for exaggerating certain spots. Xenomass is good enough in itself, and in clumps of two or three, they're worth settling preferentially and then getting the tile bonuses through the Xenonursery and Xenofuel Plant quests. That is, it does make a tile output difference.
The slingshotting and optimization practices of the outlier gamist few will still favor just paring out everything, of course. You'd have to rejigger the entire thing from scratch to be like Civ V to fix that. By that, I mean you'd have to ask every Civ to research every tech, which kind of defeats the point of a tech web.
By what you want - big outputs from some resources - that's already there. Xenomass has a version of that. Firaxite has a very of that (a few buildings that add outputs to Firaxite). If you really wanted to, you could take additional Agreements to boost that even more. Game mechanics already there, if you really want to play that way.
There's even a version of that for basic - Fungus is a decent enough tile, but it becomes way better with Growlab on Harmony. A bunch of sites with clustered Fungus is worth using for breadbaskets and gunning for Growlab instead of Vertical Farms. Yes, I have done that. It worked pretty well. Yes, clustering like that happens. I believe adding Photosystems later adds +1 food per Plantation, too, so a bunch of Fungus with Tubers and Fiber is a pretty fine site.
If you want a focus on Basics, take Nature's Bounty (+1 Production, Basic Resources), and Commiditization (+1 Energy, Basic Resources).
Thing is, playing like this is optional - you can play like this, but you don't have to. And why not? You can already play the way you say you want the game to be; what's wrong with allowing a sort of play that doesn't focus on resources as much?
If you have to sacrifice game mechanics for theme without filling it by other means then that's a very awkward trade-off to me.
You're not sacrificing anything. Game mechanics serve theme. That's the only way that's good. If the mechanics betray your theme, it's a bad mechanic.