In the end Thomas was just one person who ended up being evil. One guy.
Snyder has already infested the wayne household with owls. He's shown them dealing with them throughout their history, the owls even creep inside the manor. And if the Kanes are in it, then there's big part of the family that's in it. It's not some random Wayne in the long history of the family like Thomas was.
It just ties the family history to the owls too much. Cant the Wayne family be a normal family that didnt deal with owls and assassins and supervillains?