[Teddiursa of the Sky]

If you played Bioware or Blizzard games, you'd know that it is very easy to make a real time combat system for a game such as Pokemon. Or even look at Final Fantasy. That game series has made some marked improvements from the first pixely one from the old NES era.

Make certain attacks have different rates or speeds, like weapons in Dragon Age, Knights of the Old Republic, World of Warcraft, Diablo, Warhammer, etc. It is not like it is totally new technology that would be implemented. It would be a more action packed game, and would be very similar to the anime.

Certain attack rates? What do I mean?
A weak Electric move like Spark would take 6.0 seconds to use and would have a 5.0 second cool down time, eliminating the constant spamming of attacks.

A strong Electric attack like Thunder would take 15.0 seconds to charge and an 80.00 second cooldown time.

Also make it so that the Pokemon don't necessarily have Power Points, but have Power Levels. Where it depletes and recharges slowly overtime, or you can use Ether to replenish it.

It is so simple to think of, I have no idea how difficult or easy it would be to implement it (it takes a year at the least to develop a balanced RPG engine, let alone the graphics and such), but it is a good start.