The main area two areas I've personally noticed botania lacking are sculk sensing (Gourmaryllis doesn't trigger a sculk sensor while eating, despite clearly making noise, bergamute doesn't act like wool, etc.) and the Agricarnation (many of the new vanilla plants require bonemeal to grow, so the Agricarnation does nothing for them). There are obviously additional things from vanilla that botania could add versions of (tridents, shields, netherite interaction, trims, hoglin trading, etc.) but those are the ones that stand out as the most unintuitive.