The ideal of course would simply be to have both (preferably with some user control about using one or the other or both). While some of the functional use space they cover overlaps (as would other methods like retina scanning), it's definitely true that they have use cases which are independent. There isn't any inherent need for it to be a zero-sum game.
However, Apple is already apparently having significant trouble getting the X produced, apparently getting both into it was an impossible reach for this year, and at the end of the day "real artists ship". Touch ID was not refined when it first shipped, it got more accurate and much, much faster over time, it was merely "good enough to get the ball rolling", but at some point that stage of things is needed. It's a tradeoff that's a challenge to get right and people can argue about where the balance is in any given instance, but I think Apple has been pretty consistent about being willing to bite the bullet and get the cycle of refinement going at a stage just before full refinement, and I'm not sure they're wrong, or that the level of refinement they've managed to reach with other products would be possible as quickly without getting it out there and in real world use.