Two reasons come to mind:
1) it was already mostly done and the gap in power between 3DS and Switch is rather large.
2) They don't want to try and merge both console and handheld out of the gate since the 299 price is a bit steep for handheld only audiences so they want to phase it out more slowly and a new FE based on essentially the exact same engine as the one they just made is a fairly easy option to take.
I personally never thought that the Switch would come out and immediately all 3DS everything would die immediately; the Switch was always going to be too pricey to try and force the 3DS crowd to migrate over immediately. No, they aren't going to make that move until 1) they have the price down a bit, probably 250 and 2) they have major franchises in place to immediately give a compelling reason to make the jump. I am looking at mid 2018 as the probably point at which such a move will be made, based on the target window for Fire Emblem Switch.
Also, they will want to give Pokemon Sun and Moon time to breath and finish getting the bulk of its sales and also give Game Freak time to work on a Pokemon project for the Switch.







