One possibility is incompetence. But Boeing engineers are smart people, so I'm not convinced by this. The elephant in the room is the requirement to maintain a common type rating with older 737 models.
Suppose they did originally do what the fixed software does now, and disable MCAS if the AoA sensors disagree. The problem Boeing face is that with MCAS disabled when this occurs, the plane no longer flies like an older 737. They'd need to announce to the pilots an AoA disagree, and announce that MCAS was disabled. Now what? A pilot certified and trained on the older 737 would not know how the Max now differs from what they trained on. If they'd done this, they'd have needed to provide additional training, and this must have concerned Boeing management that it might jeopardize the common type rating. Hence it seems likely they didn't add the AoA sensor comparison for this reason, reasoning that it was unlikely to be a problem anyway. We now know that reasoning was flawed.
What does this mean going forwards? Will EASA and other CAAs refuse to certify the modified 737 Max under the same type rating as the older 737? This certainly seems possible. If they did require a separate type rating, this would likely kill 737 sales, regardless of whether the plane is now safe.