See the problem is the stealth genre is ill defined. I look at it not based on potential playing styles but the way that the AI works, which is that they try to mimic reality in that they can "see you" or "hear you" and investigate. They can be fought... or snuck past, with varying levels of success based on the level design, your arsenal, your skills and your equipment. If you can shoot, and shoot well, players who are expert FPS can take advantage of this. If you take that ability away, the game is called clunky. If it remains, it's stated that it makes it fail as stealth because you have other options.
To me, it feels like the problem here is the gamer, and not trying to act like a dick but take the designers perspective. You're given the option to play it as you wish, and if you choose to play it in such a way that's less fun to you, you then blame the game. Furthermore, there's difficulty choices that make the more aggressive strategies impossible for most players.
Trying to find a perfect balance is impossible, not because it hasn't been done, but because it's impossible. If it's possible to win with guns, then there is going to be a population of heavy FPS playing gamers that will make it feel easy. If it's clunky and slow to them, it's impossible for normal players.
I feel like for most players, who aren't adept at finding the best strategy and performing it flawlessly, MGS4 functions perfectly. For the hardcore, there are more difficult modes. For myself, I find it hard to beat it at all on the difficult mode, let alone trying to beat it without getting any kills or trying to beat it going rambo. I just kill when I have to, and sneak when I can. I feel like that's where it's the most fun and where 95% of the players who played it wound up.