Because $300 is way too much to be asking for kids. If they do it, then they could damage the userbase for Pokémon. By having it cross platform, they have the best of both.
Then, as it's also a game in the same pokémon generation, they need to work out a myriad of things such as local Multiplayer connectivity between Switch and 3DS. Online can be done relatively easily, but local is where it'll get tricky. Sun & Moon already have a separate friend list to the 3DS (calling them VIPs), but there's a lot that needs to be done.
I honestly would not have pegged a Switch game until 2019 due to the whole compatibility issue plus the increased cost. I was of the belief that Pokémon would shift to Switch down the line when a smaller, cheaper, handheld only (out of the box, dock separate) version of the device could be made and released. People ignore the factor the 2DS had on getting the 3DS out to kids and thus Pokémon. When you go to a Pokémon event, more often than not you will see a kid with a 2DS. The price point is a stickler for the younger market, at least right now.
Cross platform would resolve this until down the line when Generation 8 Pokémon games come
