Random thoughts on how to have scaled the Pokemon main series games better for the long-term. By and large, this involves scaling down pokedex expansion per generation. The key points are:
Introduce fewer new species per generation (~50 per generation after the first except gen 5 whose total-roster reset gets its own 151).
Focus on viability first, mechanical gimmick second, and never add something that has neither!
Add more evolutions, pre-evolutions, branched evolutions, regional forms, and other special transformations instead of new species.
Fewer legendaries!
Focus less on a linear narrative. Let the map open up with extra branches to explore and only a basic "main" plot with the villainous team, like the early generations.
Stop focusing on legendaries (excepting generations 3 and 4).
Consolidate Nidoran♀ and Nidoran♂ into one pokemon with gender differences. Still have it branch into Nidorina and Nidorino which become Nidoqueen and Nidoking, respectively.
https://static.wikia.nocookie.net/pokemon/images/4/46/0029Nidoran%E2%99%80_HGSS.png
https://static.wikia.nocookie.net/pokemon/images/b/bf/0032Nidoran%E2%99%82_HGSS.png
Merge the Cubone and Kangaskhan families. Start with Kangarunt, which evolves into Kangattila normally or Cubone if leveled while holding a Bone Mask (new item). Kangattila evolves into Kangaskhan and Cubone evolves into Marowak.
https://static.wikia.nocookie.net/pokemon/images/8/8b/0115Kangaskhan_HGSS.png
Remove Cascoon from the Wurmple family and make it a mid-evolution between Venonat and Venomoth.
Make Hondour and Houndoom regional variants of Growlithe and Arcanine.
Make Skitty and Delcatty regional variants of Meowth and Persian.
Make Plusle and Minun into regional variants of Pichu that don't evolve, hatched via breeding parents that are holding North or South Incense (new items). (Regular Pichu hatched if the parents are holding both types.)
Make the Aggron line a regional variant of the Ryhorn line. Remove Aron and add a new, intermediary form so that Lairon and Ryhorn are parallel, as are Aggron and Rhyperior.
Remove Spoink and make Grumpig a regional variant of Hypno.
Consolidate Volbeat and Illumise into gendered versions of one pokemon speciesl.
Make Relicanth a regional variant of Magikarp caught in the undersea cavern that doesn't evolve.
Remove Luvdisc.
Make Clampearl a regional variant of Shellder. Have Gorebyss and Huntail evolve from their respective items, with Cloyster still available via a water stone.
Make Electrike and Manectric regional variants of Growlithe and Arcanine.
Make Feebas a regional variant of Magikarp, caught outside of the undersea cavern, that still evolves into Milotic (as opposed to Gyarados). Feebas would still be caught only in specific water tiles, allowing regular Magikarp to be caught anywhere else.
Make Taillow a regional variant of Pidgey and Swellow a regional variant of Pidgeot.
Remove the Wurmple line. (Cascoon was already moved to the Venonat line.) Have Beautifly and Dustox regional variants of the Butterfree and Venomoth lines.
Make Slakoth and Vigoroth into regional variants of Mankey and Primeape. Still have them evolve into Slaking.
Remove Spheal, cute as it is. Make Sealeo and Walrein into regional variants of Seel and Dewgong.
Make Gulpin and Swalot into regional variants of Grimer and Muk.
Remove Absol.
Remove Wynaut. Incorporate its additional moves directly into Wobuffet.
Consolidate Latias and Latios into one gendered pokemon.
Remove Surskit and Masquerain.
Remove Chimeco
Make Budew, Roselia, and Roserade into regional variants of the Oddish family.
Add a regional variant of Ekans to Hoenn which evolves into Seviper instead of Arbok.
Make Mothim a regional variant of Venomoth.
Make Glameow a regional variant of Meowth. Keep Purugly as a separate species that this regional variant evolves into.
Remove Chingling.
Remove Phione.
Make Finneon and Lumineon into regional variants of Goldeen and Seaking.
Make Carnivine into a regional variant of Victreebel.
Now for some additions/changes:
Add a ghost/fire variant of Ninetales evolved at night (Johto).
Make shiny Onyx a special case where it is Crystal Onyx.