First off, there should be evolution at least from near the beginning of the game. It's bad enough to start a game in Sky as a Riolu and Vulpix just so they can evolve.
As for the plot, I'd like to see more drama. Shocking plot twists, tear-summoning moments, and suspense. I also think there should be a larger cast of characters. Maybe a clear villain, some important supporting characters, and "expendable" ones that die in action, go missing, get shattered by the collapse of a time portal etc.
Now this would totally be a stretch, but maybe more fantasy RPG effects. You know, stuff like spells and chants, giant armies, plenty of boss fights. The PC would pick up spells as items and get special effects from them (Kinda like orbs, but mostly atmospheric changes).
They should seriously make Eevee a starter only if you can evolve throughout the game. And just remove Meowth or Skitty period. That way they can afford to keep some of the Sky starters (but NOT Phanpy or Shinx) and still add the Gen V starters, Miccino, and Vanillite or something.
Just my two cents, don't have to agree with 'em.