Eh...I don't think Konami had as big an impact on the game as everyone thinks. It's certainly possible that they had an impact on the later parts of the game because Kojima was essentially sent packing, but I'd wager the bulk of the game is mostly what Kojima wanted.
I'd have to disagree about MGS2, though. I'd probably rank it as the worst of the series. Not that it's bad or anything...it's just not as good as the others. The tanker chapter was phenomenal, but the rest of the game didn't live up to that segment.
I'd rank them:
Snake Eater
Metal Gear Solid
Guns of the Patriots
Phantom Pain
Sons of Liberty
The toughest call was between MGS4 and MGSV. I gave the edge to Guns of the Patriots because, while the story fell apart at times, it felt more like what I want from a MGS game than Phantom Pain did, even if MGSV had better gameplay.