I observed, long before looking and Fabrico, that Minecraft seems to lack reasonable ore veins.
I mean that it would seem desirable (in a game about building) to be able to find enough mineral resources in a location that (even with just vanilla Minecraft) it would be advantageous to actually build a railway to the mine to carry all the materials out.
Might give a different style of gameplay if one in every 10 chunks contained a large iron ore vein, 1 in 40 containing a gold vein, etc. Would be like a factorio spread of resources, but mostly all hidden underground. That would also give a use to the BC Mining well, take a sample in a chunk, if it brings up some ore, somewhere down there is a rich vein to dig up.
It sounds like you want Custom Ore Generation. The clouds distributions were designed to be "You'll have to make a railway to the cloud to mine it out"; the veins give you those "rare chance of a large ore vein", etc. (And: Large ore vein: An iron vein that doesn't twist can stretch 10-12 chunks, easily.)
Note that it was designed around old (125-164) biome layouts; it broke badly with the 17x world layout. The lack of snow zones, and deserts, combined with the huge abundance of forests, ruin the balance.
It just means it is something I have to consider every time I add a mod to my pack. Especially if it has world gen, since the only fix I'd be allowed to make would be removing said mod. ... Given the world gen in many of them adding and removing mods with lots of world gen would leave the players with nasty looking worlds and isn't a very good option.
This very concern -- worldgen changes -- led me to a policy back in 125, that I softened a little in 147. No mod worldgen blocks in the overworld. At all. Period. No exceptions. (In 1.2.5, I did not allow any mod blocks, or any mod worldgen in the overworld. I changed my view with things like Rogue-like dungeons, which only uses vanilla blocks, just arranged a little differently. The dungeons still work without the mod.)
If I cannot load the overworld into vanilla minecraft, without it being ruined, then the mod does not go in.
Now, I'll tweak the mod with other tools. For example, I can use Custom Ore Generation to replace beehives in the overworld with dirt. (Sadface; I can't replace some with air, some with water, or others with rock; but dirt works well enough in all those cases). The result is good enough -- some odd lighted, glowing dirt blocks, but those clean up like other lighting bugs.
Equally, nothing changes Twilight Forest, except for putting in COG ores. (Did I mention that I hate vanilla ore gen layout? I've used COG since I first ran into it in 142.). Everything else for mod generation is in mystcraft ages.
The benefits? Well, first and formost, if a mod dies, or does not update, or worse, updates but fails to transition from 164 to 17x ("sorry, I expect all users to start a new world every version"), then only the disposable ages are damaged. The world itself can stay just fine. The second benefit? Everything has a purpose. Twilight forest is it's own play style. Overworld has dungeons. Ages have all the mod things to find (plants/flowers/bees/etc). And the more "biome-dependent" those are, the better -- the more and different ages to explore.
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The observation that Twilight Forest is balanced around vanilla, and is destroyed by most tech mods? Sure. I'm aware that when Direwolf's playthrough gets to the forest, he strips himself of the high-tech stuff. I'm planning on setting up my server for 1.7.10 with us starting in the forest, and not getting to the overworld until ... Well, I don't know. I figured out how to "Gate" mystcraft out to the point of very unlikely to get to it from the forest -- require an emerald in the book binder's recipe. (No villages, and no extreme hills ...).
Machines that ruin balance? Reika even mentions that RoC destroys the balance of TF. Well, yes and no. The one, and probably only, design philosophy of Reika's that I disagree with at this point involves the bedrock breaking ability. Minecraft has one "admin" block, that doubles as the world border block. It defines the bottom of the map, that you cannot go through. RoC treats this as another resource, a very hard to acquire resource. But there is no distinction between the "natural, mineable" bedrock at the bottom, and any "admin blocks" that are walling off other areas. Now, with the changes in 1.7.10 -- doubling the power needed for the bedrock breaker, removing the bedrock ability from the borer, eliminating the "chain water engines to power anything" feature, etc -- this might no longer be a concern. I'm not even sure if you can get the resources for jet fuel in the forest.
RoC's tech tree? People who want to replace bedrock with compressed cobble? Sure, trying to change any portion of the tech tree will give you all sorts of headaches. But what about individual blocks? Would disabling the extractor be a problem? Would disabling the borer be a problem? Would disabling the gravel gun be a problem? How about limiting the maximum power that can be put into the gravel gun?
I've done a small amount of "semi-creative" testing in 164, on 21-25. Give myself a large but fixed supply of iron, and as much of the rest as I need. Peaceful mode, survival, and try to build. RoC consumes iron so bleeping fast it's ... it's like the mod assumes that you have an automated supply of iron (borer), and can increase your supply from that (multiple machines to multiply ore). So it's not just gating by what you've managed to build, unless I'm way off, it's also gating by resource acquisition and assuming you've got ore automation. And as soon as a mod assumes massive ore automation, suddenly every other mod's ore costs become artificially low.
*THAT* is my big "balance point" concern.
Yes, there comes a time when you've basically "won" the game. Heck, even vanilla has beacons. Got the ability to do just about anything? Fine, here's an "almost creative" play mode for you now. No problem. And, the truth is, from what I've seen, the "what it takes to run the extractor quickly, what it takes to make a borer that produces lots of stuff for the extractor, what it takes to get the output from the borer, to the extractor, and to sorted storage", you're at "end game" by the time you get a large output from that stuff. It's the point where you don't have it all quite operating fast and smoothly, but are still on the 3 times, or a manually switched 5 times that requires either baby sitting or a smart redstone controller (hmm, I just realized I never played with a comparator and the extractor -- what does it detect/report out?)
And note that even without that "late end game", you still have the whole "I have to go now, instead of closing the game, I'll just AFK in my base until I get home" factor. More than anything, this is why I dislike automated mining / why I think it doesn't fit vanilla minecraft. You go from "earn X resource every Y units of play" to "Here, have infinity, or at least a double chestful." It's like a server with chunkloaders, only in rotarycraft's case, the borer will chunkload a full chunk itself -- and how hard is it to get all the processing into that one chunk?
Does it make sense to say "I no longer want to be concerned with mobs"? Bedrock armor, massively charged gravel gun, heck, the bedrock axe changes certain terrain features from scary/spooky to "beh, nada". Is that "late enough" that you have to "win the game" before you can get there? Can those things be pushed earlier or later in the tech tree to balance what a given server / player wants? Are they currently balanced based on what/how Reika wants to play, and does that balance match how other people want to play? (Reika has said he searched for a rainbow forest biome -- and designed them as non-mob, farm-animal rich -- because that was how he liked to play, without having to deal with mobs all that much because he did not like vanilla's combat system)
For example, if magic bees gained the ability to produce jet fuel, or magic crops gained a bedrock dust crop,
Well, maybe, maybe not. You have bees that produce lubricant, and require canola plants as their flower. I don't know jetfuel well enough, but it does require pretty much everything -- something in there could probably be made into a "well-gated flower". Perhaps using jetfuel to light fire-resistant netherwart on fire to make a new flower for the bees? Bedrock dust ... ok, it's harder. Anything that requires bedrock can be obtained just by digging a hole, there is no distinction between "player placed bedrock" and "natural bedrock". Unless maybe you had to sprinkle bedrock dust on a vanilla plant to make a bedrock plant ...
Point is, mod isolation may be one answer, and it may be the easiest answer; it might not be the only answer.