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[PatrikLundell]

It's a bit silly that spores released from caverns can result in corresponding plants everywhere except the caverns above. As long as the corresponding plants have their growth requirements met (such as savagery/evil/good, none of which currently affect vanilla subterranean plants) they ought to settle in the caverns above their native one as well.
There is currently a water access requirement for all underground trees except blood thorn, but if the drifting water vapors within a fortress is sufficient to support those on muddied rock everywhere, that ought to be sufficient for upper cavern growth as well.

[FantasticDorf]

From a gameplay perspective, inadequate handling of mud is a world generation issue, and that much of the caverns may end up being barren rock and actually habitable areas where spores can propogate are far and few between is more arguably realistic than the entire cavern itself being full to the brim. So to some effect it already works as intended, and the plants often grow wherever there is a decent distribution of mud, if anything its more of a complaint that there is such a static habitat and these areas identifiable as 'barren' rock caverns and slight more lush fungus groves aren't codified more deliberately to break up the terrain a little bit.

If you look at the caverns in legends mode they are all one big complex, in some respects it really needs splitting up like the overworld into larger biomes rather than entirely divisible on creature & plant diversity by layers.

[PatrikLundell]

From a technical perspective the caverns ARE split up in multiple biomes just like the surface (examine df.global.world.world_data.underground_regions). It's just that there are only two different underground biome types (Subterranean Chasm and Subterranean Water), which seems to correspond to normal caverns and mud covered mostly barren ones, as blood thorn can live in both (provided it's also the 3:rd cavern), while Spore Tree can handle only Subterranean Water). Plants and creatures are then locked to cavern levels in addition to the one (or both) cavern biome types they can handle, and there's some randomization as to which things show up in which cavern biomes (with some not appearing in any of them, at times).
However, cavern biome variety is a completely different topic (and harder to address) than spore spread application.

I'm certainly in favor of additional cavern biome types, as well as bare rock stretches, and other additions/enhancements to spice things up, but those belong to a different suggestion topic.

[FantasticDorf]

I always thought it was actually air from the surface permeating downwards into the caverns when it's broken into that causes the spores to suddenly become active and rush upwards and around from the lower layers, it doing it itself in world generation wouldn't be realistic at all or atleast shouldn't travel very far from the entrance.

It'd be a bit of a early warning where entrances might be before the monsters crawl out of it and you meet them first.

[PatrikLundell]

Sorry, but you've completely lost me. I have no idea why the fact that caves reaching down to the caverns doesn't release spores (which I think is what you're talking about) should have anything to do with whether spores traveling from lower caverns to upper ones when the player has created a contact between them can grow in all suitable underground locales except those upper caverns.

[NW_Kohaku]

Well, if the cavern occasionally flooded the way that the old underground river would flood, it would create a good reason why a cavern is pristine and mud-covered before you come along, then is barren afterwards.  (It'd also make for an interesting event from an engineering standpoint, but it would also, of course, require that it have some sane checks to prevent the WHOLE cavern from flooding and killing all the creatures off....)

Toady also wants to make it possible to plant trees (including the mushroom "trees" in the caverns) in the future, which would presumably be a better time to add limitations on the spread of "tree spores", since if "tree spores" didn't spread to near-surface soil-layer caves, they wouldn't be able to spread out of the caverns at all. If players could take some sort of seeds up and start deliberately seeding their own artificial caverns for "forestry", then having them stop spreading quite so universally would make sense.

[PatrikLundell]

Yet another post discussing something only vaguely related to the suggestion, more complex, and applicable to the far future...

The current mud covered caverns are static Subterranean Chasm biomes, unfit for most non moss growth (I think only blood thorn is excempted), while normal caverns are of the Subterranean Water biome type. There is currently no in game mechanism for them to change from one biome type to the other. Future development on making caverns more interesting will probably touch on that as well. However, that discussion has nothing to do with the suggestion.

Introduction of player tree planting doesn't mean natural tree reproduction should cease. Artificially restricting tree spores from spreading while allowing moss (and shrub?) to do so would be odd, but I wouldn't be opposed to having the plants' level restrictions apply to the fortress as well (meaning that e.g. blood thorn wouldn't grow higher up than the top of the third cavern, for instance), based on a mystical reliance on some kind of level property (air pressure?). Player tree planting might override those restrictions in the same way player planting currently allows growing of evil/good/savage crops in biomes without those properties provided the biome restrictions are fulfilled. Again, these changes are far larger than those suggested (and the suggestion was made to allow it to be implemented without replacing a lot of game infrastructure so it could be performed in a reasonably near term).