I think this article sort of misses the point.
FO3 isn't a shooter - it's a roleplaying game with guns.
If it had focused more on the shooter mechanics, it would've risked turning into a shooter with some RPG elements.
As an avid and long-time player, a lot of what I appreciate about FO3 is that, with VATS, I don't have to be always on edge and focused on my own reflexes - I can relax and focus on roleplaying, and when combat happens, it's more a matter of the character's skill than my own, which is how it should be in an RPG.
And if I want, I can forego VATS and handle it like a shooter. And yes - it's not as good that way as a dedicated shooter is, but I wouldn't expect it to be, just as I don't expect the racing in a GTA game to be as good as the racing in a racing sim.