I disagree, like in my examples, in The Getaway and Gears of War, it's pretty fast too. It's just an extra animation and it would add to the gameplay as you can't shoot and pick up a gun at the same time. I think it should change. The game has evolved over the iterations, something like what I mentioned will add to the gameplay.
It's just that Kojima did a great job in so many areas (the sound fx are excellent...), and there are some realistic aspects (massive recoil from the sniper rifle), that these sorts of things stick out. Same with the barrel coming out of nowhere. I'm not saying they should change everything, just add some polish in the areas where they can...that's all.
I don't know about you, but when I watch the vid I'm completely immersed in the world Kojima has created. Almost as if I'm there. These little things like walking over weapons reeks of last gen and doesn't match the standard the rest of the game has set and adheres to. To me, anyways.