If the other mod checks the block's isReplaceableOreGen(...) method or checks the Ore Dictionary to see if the block is registered as "stone", then ore generation will work just fine.If that mod uses world.getBlockState(...).getBlock() == Blocks.STONE, then that mod is not compatible with any mod that adds custom terrain generation and will not spawn ores in the world if Minecraft Mineralogy is installed. The solution then would be to install Base Metals and create an orespawn file to tell Base Metals to spawn the missing ores.
Note to mod authors: the isReplaceableOreGen(...) method is preferred because Ore Dictionary look-up can become a performance bottleneck.
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My mods: Base Metals, Power Advantage, Steam Advantage, Electric Advantage, Minecraft Mineralogy, Dr. Cyano's Lootable Bodies, Dr. Cyano's Wonderful Wands & Wizarding Robes
The new rock slabs in the 1.9 version can be placed vertically to be used like walls. If that is acceptable, then I can backport that feature to 1.8.9 pretty quickly. If you want true walls, then what I'll do is add them to 1.9 and then try to backport version 3 rather than update version 2.x
EDIT: Note that I changed the registry naming formula in version 3, so if I backport the whole version, then there's a good chance that updating from 2 to 3 will destroy your world (by making all the stone in the ground disappear).
Little problem in survival... each of the stone types are NOT breakable with a wooden pickaxe. Well, you can break them, but it doesn't drop any block.
That makes getting stone tools ridiculously hard, as you'd have to lower creepers near the stone get em to blow up without killing you, then collect whatever stone there is and use it to make a stone pickaxe.
Not all types of rock are the same. In similarity to naturally occurring forms, some are easy to break and some are pretty hard. So likewise, you'll be able to break some easily with wooden pickaxe, and some you'll need an iron one for (at least for any decent speed of digging). You can look up the hardness on the Dr.Cyano's wiki or on a real world wikipedia as I think he tried to stick to real life stone properties.
In minecraft this can lead to somewhat increased difficulty at the start, but really very little once you know to expect it. Any type of rock you do dig up, will function as regular stone when it comes to fashioning tools and weapons.