They did? I didn't notice. Also, the dichotomy that you're looking for is Science vs. Faith, not Science vs. Magic. Magic is just science that we don't understand yet. I think that the subject of Science vs. Faith would be an interesting one for the games to tackle. Being Pokemon, it would be done in a relatively simplistic way, but that would likely be for the best.
My NIDOKING brings all the boys to the yard: http://goo.gl/ExAoe
It would be interesting, remember in Arceus and the Jewel of Life, when Ash went back in time, the group of people in the previous culture referred to Pokemon as "Magical Beings", could be that there is a group of people that still refer Pokemon as "Magical Brings" and want to keep them for themselves.
But that's me thinking the way I do.
B**** don't make me HM01 you! ALL HAIL THE GLORIOUS HYPNOTOAD!