Numbers upgrades are fine if they're used to make mechanics dangerous instead of trivial, such as making you actually have to dodge that telegraphed attack that you used to just take to the face. It still adds gameplay and does require the effort on the developers part of tuning individual mechanics rather than just tuning up a scalar.
This works best in games where you can't upgrade your defensive stats regularly/at all or where the developers tune the numbers around the upgrades you're expected to have at that point. Also there should only be 1-2 levels of these kinds of improvements, otherwise they should really be adding additional mechanics.