The Meaning of Life, the Universe, and Everything.
Let me start with a little context here before I tell you my suggestion. My favorite resource/texture pack out of every one I've used is Chroma Hills. But obviously Chroma Hills doesn't have support for mods. Making it a bit disappointing playing to game using Chroma Hills and coming across untextured blocks. So I suggest when designing your world gen blocks like ores, gems, etc. Rather than creating a whole new block.
Instead you create an overlay. And when the game starts to generate chunks it'll randomly pick stone block within that chunk and designates that stone block to be your ore. So your overlay is placed over the stone block. And when it is mined instead of popping out a piece of stone, it'll pop out your ore. Obviously you wouldn't be able to do this with custom trees and flowers.
But I think this would be brilliant for ore generation. This way I can still play my game with the Chroma Hill texture pack and the mod would still blend in seamlessly without worrying about weather or not my favorite texture pack has mod support or not. Anyone feel free to make suggestions or discuss this idea.