Thank you for the in-depth writeup! I echo a fair few of the ideas/suggestions laid out here, so below will only be the ones I have additional thoughts/a different take on. I'll start with just base Botania.
Alchemy:
Can do away with shrub cycle imo. Even ferns can be bonemealed and broken to dupe them (via shears, or whatever mechanic we end up with for other plant matter like vines etc.)
re. berry cycle, it'd be nice if there were a way to encourage Apple drops somehow. Even then, they're useful for only three Botania recipes: Soul Cross effects, Absorption pot, and player heads. I think just having a Agri-boosted Oak farm is probably enough, so imo another cycle that can go.
Fish cycle. Can also go, it's not like fishing can really be automated anyways. Marine Allure exists, and if a player really hates fishing, Cocoons in water would do the job. Anyways, the Brew of Gills outclasses vanilla water breathing pots and takes Prismarine instead.
Honestly I doubt 90% of players would kick up a fuss over the 1.17 stone types being a cycle despite not really fitting together. There's a case to be made for Talc -> Calcite and Gneiss -> Tuff given the former are both minerals and the latter can both (kinda) be classified as sedimentary rock, but it'd "unbalance" the metamorphic stones, so to speak. Might be good to brainstorm this a bit more with the rest of the community?
With the flower cycle, in addition to the floral fertiliser bedrock parity idea suggested, perhaps when applied to Enchanted Soil, any kind of vanilla flower (minus sniffer specialties and wither rose) can show up on there, ignoring biome restrictions. Or the different pasture seed grasses could support different vanilla flowers when bonemealed/floral fertilised?
Rotten flesh to leather. I think it could cost a bit more and still be good.
Poisonous potato -> poisonous tater could be a neat hidden alchemy recipe.
Gravel -> flint -> gunpowder for entro automation in vanilla+botania is painful. Could remove if only creeper spawners were in vanilla, or you could somehow influence what a spawner spawns (maybe with a mob head?)
Big fan of book and quill -> name tag.
Finding slimes in vanilla sucks, and cactus isn't used for much else anyways. This is one of the classic alchemy recipes imo, it'd be nice to see it stay.
I've mentioned this before but I find almost every deconstruction recipe pretty useless, other than Wool -> String. It'd defo reduce the bloat in the lexicon entry at least, and make more space for other recipes if needed.
I like the sound of a Basalt -> Netherrack -> Blackstone cycle
On the topic of GoG and additional recipes - I went back and checked 1.7.10's GoG modpack. I do appreciate how to this day, the number of changes GoG makes are minimal. Any extra recipes should reduce aimless void exploration and circumvent the need to wait for the wandering trader:
- Crop cycle could go if there's an alternate way to get cocoa beans and beetroot. Building a mob farm is part of GoG's gameloop, and chances are you either kill a Zombie and get a potato/carrot drop, or you cure a zombie villager. I guess it kinda sucks if you manage to get pigs from your early cocoons and can't breed them. I guess it can stay.
- Can probably make the sapling cycle cost the same as crop cycle.
- Re. flower cycle, could be removed if above flower cycle suggestion implemented or something along those lines.
- Froglight cycle isn't needed on GoG either. Most biomes will spawn Temperate frogs from cocoons, Nether biomes produce warm frogs, and the End produces cold frogs. It's just a matter of bringing them home and setting up a magma cube farm.
- Blaze rod -> nether wart would be crazy useful for a void nether run, assuming fel blazes drop rods in the nether and structure compass is past elven or end tech.
- Probably want a way to get Bamboo a little easier. Perhaps Sugarcane <-> Bamboo with the same cost as crop cycle? Maybe that opens up cheap endo fuel a little too soon vs tree farming. Kelp <-> Bamboo seems slightly better.
- Can remove the Heart of the Sea recipe with the Loonium changes, assuming we get a structure compass of sorts.
It's worth reviewing the rune and flower recipes too, so we can make sure those remain automatable and maybe update some sticking points. There should be a post floating around on the forum addressing exactly this.