They probably decided "we want to (soft) reboot the franchise!" Which is something Pokemon always seems to do every odd numbered generation. Generation 3 was sort of a reboot, as well. Old Pokemon weren't in the first few routes of the games. But, it's definitely because Game Freak wanted to reboot the franchise again. Also, Unova is extremely far away from other regions while Kanto, Johto, Hoenn and Sinnoh are likely not too far away from eachother. That was probably done deliberately, though.