I mean the Switch is clearly the reason for this. Quite frankly, I think Nintendo may be mildly terrified of the prospect of the 3DS getting a massive second wind that basically undermines the Switch's popularity as its successor. They know how important the Switch launch is and they probably had a monkey wrench thrown into their plans with PoGo. There's absolutely no way Nintendo could have planned for PoGo to happen back when they were outlining their strategy for selling the Switch. They probably assumed they could kind of phase 3DS out after this Holiday and all attention would be on the Switch. Well now Pokemon is a phenomenon again and Sun and Moon have made the 3DS a hot ticket item again. So they're purposefully trying to supress the 3DS demand by not supplying enough to meet it.