-More distinct differences between verisions.
All players are supposed to be enjoying the same world at the same time. You're not supposed to pick what faction of the pokemon universe you want to enter, you're supposed to pick what version exclusive pokemon you'd rather find in the wild.
-A more advanced levelling system.
Have you even tried utilizing EVs or IVs? If you think levelling a pokemon is easy, you've naver RNG'd apokemon for competitive purposes before.
-While we're at it, let us level our trainer too.
Pokemon would become just like every other RPG once the focus is put on the character. Everything in Pokemon is meant to progress in a relatively set path, save for what stats you focus on while raising your pokemon. As the player, you grow enough on your own by gaining trusted friends as the Pokemon you journey with and gaining badges. The badges themselves unlock passives in the overworld and used to give your pokemon mild stat boosts in battle.
-A story that isn't the same.
They have a formula that's made them money for years now. Your suggestions of death and regret are way too dark for kids to handle regularily in-game. You do know that the games are geared towards kids, right?
-something about a new game
You don't sound like a competitive player. The replay value lies in raising more pokemon and entering wifi battles to gain a sizeable winning streak.
-Evolve the battle system
The present battle system involves damage calculation between four different stats, speed priority, type compatibility, same-type-attack-bonuses, attribute resistances, weather, stat boosters, stat swappers, priority changers, The ability to coordinate a strategy in three general situations and over ten specific situations...what was so simplistic about the battle system again? As far as your complaints about type compatibility goes, the game is supposed to teach you about balance. If your entire team has a crippling weakness to one particular attribute, then it shows where your weaknesses lie as a trainer. In the metagame, every pokemon is there to serve a purpose in battle, and most are trained well enough and given the necessary techniques to cover their weaknesses and stay in the battle as long as possible. But that's what having a team is for. You make it sound like you trained a team full of Charmanders only to get in trouble when somebody pulled out a Boldore and Basculin. Positioning exists in the three-on-three battle formats, and that's all a good player needs.
-sigh- Casual players just don't get it...