I'm not a resource pack maker however but I have had support many behind the scene. This is personal choice i think, but without following any form of list of number or A-Z, you will get lost in the long run. So I usually follow block ID or name.

per biome but when one of these blocks is in multiple biomes the order becomes a mess.

doing it by biome is good to filter a pseudo atmosphere for example, I can take all nether blocks and filter them with warm colors or I can make similar draws between some blocks like magma and blackstone or magma and netherrack

i remake textures at the same time if they share a pallet so i dont forget

I usually make textures depending on what I need and what it connects to. So By Theme is what I would say I make textures by.