Kojima would've been able to put out a complete version of the game if Sony would've allowed him to release it on two Blu Ray discs like it should've been.
I don't think he did fill up 50 GB.
But one thing he could've polished out is the stealth gameplay as you said. I need an incentive to use the tools he's given, because you can breeze through the game without using them. The game engine could've been better too.
There is so much that could've been fixed. But I really can't be bothered to write them down. The same goes for MGO. It's flawed in so many ways, especially the body mechanics. The idea and execution of the online play and features is brilliant. But technical blunders really tainted the game.
Rockstar: Announce Bully 2 already and make gamers proud!
Kojima: Come out with Project S already!