There’s a lot of legendary stories that pretty much ruin each other, the Arceus vs. Mew thing being the biggest one, but what about Groudon/Kyogre and Regigigas? I personally don’t like the whole “pulled the continents apart” so I refuse to acknowledge its existence. What would you do with that story if you were in charge of all that?

Hrm.  I don’t think there necessarily has to be a conflict between the two; we can assume that Groudon raised a single Pangaea-like landmass out of the ocean while Regigigas was responsible for dragging the continental plates into their present positions.  Basically, Groudon and Kyogre are primordial beings, while Regigigas is from a more recent era.  Alternatively, though, since I don’t think we’ve ever seen direct evidence of Regigigas’ power, you could suggest that “towing continents” is a simple exaggeration.  After all, the image of Regigigas running around the face of the planet, dragging India a few metres northward before nipping off to shove the two halves of North America a few metres closer together, is just a little bit absurd.

I think my first assumption, if I wanted to keep the continent-towing, would be that there are multiple Regigigas, dragging multiple plates in multiple directions and often working at cross-purposes (hence earthquakes and such).  The second would probably be that they didn’t come to exist until long after Groudon and Kyogre went to sleep.  They’re not elemental forces in the same way that Groudon and Kyogre are; they don’t drive continental drift for the sake of continental drift.  Rather, they generally have some reason or another for dragging a continent – moving it to a warmer or cooler region of the planet, or further away from a rival Regigigas.