There should be a few more relationships between Botania and Pixelmon and Astral Sorcery and Pixelmon.

Some ideas include allowing Botania and Astral Sorcery to produce or duplicate Pokeballs using their various gimmick creation methods (runic altar, mana catalyst, starlight infusion etc) or allowing them to produce Pixelmon-specific ores.

Botania has potential in producing leaf stones; Astral Sorcery has potential in producing sun/moon dusk/dawn stones.

Additionally, it might be valuable if players can produce XP candies or rare candies (although that is a dangerous road to take if they over-automate it), or duplicate max mushrooms, or wishing star fragments. Certainly it would be good if they could produce evolutionary items, or single-use held items, which are less exploitable.

I also like the idea of potentially using them to summon entities- I'm not sure if that's possible through a relation with gateways to eternity.

Certain Pokemon should have their rates boosted or only appear around certain structures in the mod, such as the mana pool or rosa arcana or lightwell/marble.