Kojima in many ways has shot himself in the foot with a good amount of long time fans with the many, many issues such as the decision to go open word, the David Hayter debacle, the Quiet controversy, and the murky (and juvenile) promotional campaigns to name a few. Unlike past MGS games, Kojima himself doesn't seem to have the game set in stone (remember this game was originally for the PS3, not current gen consoles) and at least at this point, it seems to point out that all he wants to do is make is Peace Walker 2 and a glorified tech demo for the FOX engine.
Long story short, Kojima could have easily avoided all these but he choose not to. He is either a) Trying to prove a point. b) Tying in the controversy of the game to match the themes of the game, or c) He's well on his way to be certified fruitcake that a lot of people have been saying he is.
Rising is a different beast altogether, it's a Metal Gear game developed by Platinum Games with a good amount of creative control but a very, very punishing development period imposed on them. They could not screw this up or they'll risk a) The Rising series never picking up steam, or b) Termination by Kojima Productions.
The end result is a game that really acknowledges itself to be silly and nonsensical, but with a heart of gold, Platinum pulled this off impressively. You're not supposed to have a hard time sleeping because the plot was "bad", you're supposed to have a hard time sleeping knowing the fact that you've just cut a 65 foot tall robot into pieces with blaring techno/metal/dubstep music as if Platinum Games is shoving a toothpick in your mouth whispering "dude, you're cool."
Sometimes, just sometimes it isn't about the latest technological achievement or the grandiose plot, it's the pure, unadulterated tried-and-true methods that works best in generating a smile, and boy does Rising made many of my buddies smile when they come over.
P/s: I hope I don't have to type this long again. Phew.