Colloseum and XD already one-upped it. They're technically spin-offs but still.
Last I checked, Colosseum and XD: Gale of Darkness are indeed part of the main series proper. Spinoffs don't use any of the same battle systems as the main series, and the battle systems of the main series are only ever used in the main series proper and supplements to the main series (i.e. the Stadium games and Battle Revolution). The usage of the full RPG genre makes Colosseum and XD: Gale of Darkness's placement in the main series proper quite clear (especially XD: Gale of Darkness--it doesn't have any game modes or mechanics that would fall into either main series supplement or spinoff title).
They're both listed as a spin-off on the official site --- Serebii from the amazing Serebii.net Your #1 Source for ALL Pokémon Games & Anime info as the top online Pokédex & Attackdex!
Though thinking about it now, Pokemon is the only non-strategy games I can think of that is still stuck in the days of 4 direction tiles.
The deliberately-retro Final Fantasy spinoffs do the same (I refer to FF4: The After Years and FF: Dimensions.) --- Creator of Jay's Journey (see quote!) "It's not ten years old! Therefore, it sucks!" - Nostalgia whores everywhere