I actually like the current setup. You have the NatDex order, AKA order these mons were introduced IRL, AKA the number used to refer to the mons. And then each region has it's own dex, where cross-gen evos are next to each other and mons are numbered(theoretically) by how far into the game you'll encounter them. It's not a perfect system, but I think it's the best that can be done. The other options are renumbering every single mon whenever a new game comes out, or just ad-hocing it, and I think both of those are bad ideas.