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Now with all these new Pokémon, forms, regional variants etc, it is not fair that some Pokémon like Nidoran or Plusle/Minun have different Pokédex entries. I also think it's weird that Preevos like Pichu, Clefa etc. are 100 positions far from their lines. Same with evolutions.
I would also include entries for mega-evos.
I also don't like how it is split by "games discovery" rather for technical than lore reason (I mean, they were added to the games). I find very random than Bulbasaur is #001 and #Rowlet is #722. Ok, I understand the reason, but still I don't see it natural.
So how would you sort all the Pokémon in a more natural classification? Fossils first and legendaries at the end? By type? First all the starters, early bugs, early birds, early mammals etc... Just some random ideas.
I hope I explained it well but I have always believed it was needed a restructuring of the National Pokédex (this is another question, why national? Are all the regions from the same Nation? Is there any "world Pokédex"? how Pokémon would be sort out on this one?)
Also, which kind of information do you think it should add? I think longer entries and talking about the different variations of forms, how to change them (in the possible cases... at the end all this was already "discovered" so the Dex should be a tool to guide new trainers)
And just like a last concept, it would be very interesting a "global pokédex" with actual small variations of Pokémon based on real world locations (a la vivillion but with all the Pokémon) and this Pokédex can be like a wiki, every trainer can add some new information etc. But that would be another game probably haha (just an idea, because at the end Pokémon is from a Pre-popular-Internet era and now what really matters is collaboration and communication, which is also what Pokémon is about). Just some thoughts about it. Maybe a real MMORPG Pokémon game could be this. Pokémon GO is such a waste of potential haha