Well, I was thinking: I would want the way the Pokedex works to be completely reworked to be more like how it works in the anime. The Pokedex starts off completely empty, and gets updated as you play maybe something like this: When the trainer meets a new Pokemon in a battle, the Pokedex pops up, gives the name of Pokemon and Entry #1. Upon capture of said Pokemon, Entry #2 is unlocked, height and weight. Entry #3, #4 and so forth are unlocked after using or facing said Pokemon a certain number of times. Thus, for the Pokedex entry of a Pokemon to be fully unlocked, you have to have captured it and meet/use it often enough.
For the location/habitat entries, I know how useful it is to have all data to be available for you so that you can catch them all, but there's no challenge to it, imo. It makes no sense to me how you meeting a Rattata on Route 1 would suddenly allow your Pokedex to know that there are also Ratatta in Routes 3, 5 and 17. Or you facing the first Gym leader with a Scyther would let your Pokedex know that there are Scyther in the Victory Road or Route 27. I'd prefer it if the habitat/location list gets filled out as you meet wild Pokemon, and only on that spot where you actually met them. Which means that, if you meet a trainer with Mareep in Route 2, although Pokedex entry is unlocked, habitat data isn't. If you meet Mareep in the wild in Route 5, then it would add Mareep's data to Route 5 habitat/location list only. That means it could have been be found in Route 4, you just were not able to. This, together with expanding Pokemon availability in multiple locations (I don't like how sometimes a certain Pokemon can only be found in a single location. It makes sense more for Murkrow to be found in Routes 11-18, rather than just Route 13 with a tiny patch of grass) makes the habitat/location list unique for every playthrough.
I mean, that would be kinda cool and realistic imo. I mean, it's obvious that the Pokedex updates itself based on what you encounter. If it just downloaded the data from the Internet or something, why wouldn't you have it download everything right from the start? So it's logical that the Pokédex wouldn't know that a Pokémon lives in a certain area if you never saw it there. Besides, I think I remember having a professor tell me that they wanted me to use the Pokédex to map out the locations of the different species of Pokémon. Still, I dunno if that would be worth the frustration of the Pokédex losing the function of telling you where to find that cool Pokémon you saw once and really want to get.