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The games from the first two generations have a good story. It's a simple urban adventure with a boy stepping outside home to see interesting places, meet interesting people and grow/improve himself (this last part represented by the pokémon party and the league challenge). It's much like EarthBound where this experience is more important than simply beating the game or reaching certain objectives. For this, the story of Kanto and Johto is perfect as it is.
The anime managed to translate this pretty well into a show, until it had to stop Ash from growing properly so it could run forever. Most of the early episodes are good on their own and even many of the episodes from the later seasons too. It's the moments when they had to deal with over 20 years of going nowhere that made everyone (except for the producers) suffer.
But if that is not enough for you, certain spin-offs like Colosseum/XD and PMD or the various manga/doujin offer more straight-forward stories with the usual good, bad and ugly characters with conflicting goals and ambitions.
Or if you want, I can post a short comic about a Gardevoir who looks like that.
