I feel the music, art direction, design, and structure of the game were top notch.
I thought the shooting was fine. The stealth was great; I actually enjoyed it more than any MGS game I've played to date (1,2,3, and 4). Everything this game set out to do, it did with distinction, except in two areas.
The AI and voice acting.
Enemy soldiers were making some really, really dumb decisions. I went Rambo most of the game, all guns blazing, and they consistently made really bad tactical decisions. Hide in a doorway, watch everybody bunch up around said doorway, throw a grenade. I felt incredibly cheap, but this happened countless times during the game. As for the voices, well, I don't think I need to explain that any. Sarif cracks me up every time he talks.
And of course, the boss fights are a travesty. I'm sure we can all agree on that.
Only the first boss fight was bothersome, and even then, it wasn't very hard. As soon as I got access to the heavy rifle and piled some upgrades onto it, I literally ended every subsequent boss encounter within 60 seconds of it starting.
But I will agree that they could've been more fun or inventive.