But stealth, at least in its current form, isn't something that can simply be integrated without making substantial concessions elsewhere in the design. You lose the ability to mount stores on hardpoints on the wing, for example. That reduces the variety of munitions the aircraft is able to carry, which in turn makes it less flexible and adaptable to new missions.

Your argument that stealth is just the way things are now implies that stealth, as a feature, is more valuable than the features you have to give up to get it. The article is arguing the opposite -- that stealth is less and less valuable as radar technology improves to counter it, so maybe it's not worth giving up that other stuff to have it. You disagree, that's fine, but that in and of itself doesn't make their reasoning "flawed" and thus able to be ruled out with a wave of the hand and a jaunty "stealth isn't going anywhere."