I... don't really see the point of this. I mean, it's a game. They're pieces of data. That's never going to change. There's already a "bonding" system, it just matters more to some than others. It's possible to get an emotional attachment to them, yes, but they can't get attached to you until Artificial Intelligence is used in the games, which seems a bit of a... waste.
The game has a fun system of play for an RPG, which is the appeal. That, and nostalgia. While I'd love a "realistic" Pokemon game, I don't think I'd ever like it more than the original.
Also, I don't really understand why you're citing the anime's style of battling (or the manga(s), if you went there, at some point), when it's based off of the games, not vice-versa.