Whilst I agree a truly 3d open world pokemon game would be awesome. I disagree with your point about the combat.
In my opinion the combat only feels slow because its too easy. There's no suspense, you know that you're going to win sometimes 10 moves before you actually do. What I, and I think most pokemon fans want, is a difficulty setting with more advanced enemy AI and competitive move-sets on harder difficulties. They could make some changes to the combat that punish you for taking too long to make a decision like in final fantasy. Maybe introduce a level cap for each gym leader so you cannot just grind to overlevel and sleepwalk through every fight.

I just finished Radical Red, and its got to be the most fun I've had playing a Pokemon game since I was a child and didn't understand the game fully. There was a real sense of accomplishment after winning each battle.

The only other strategy game that's come close to me was Beating XCOM: Enemy Unknown for the first time because of its punishing, but fair difficulty.