I think the balance is interesting. The game is absurdly -biased- towards non-aggressive gameplay, such that not killing enemies and capturing them instead whenever you can is heavily encouraged (I'll even say you're pressurized into doing that), and even then capturing enemies without injuring them is even more beneficial because then they do not have to spend time in the infirmary. This means that for most normal missions, having non-lethal weapons is always preferable.
At the same time though, the game does not particularly force the player to stealth the game. Obviously playing the game with good stealth makes the above mentioned much easier to achieve without the risk of having to pull out a rifle and shoot everyone if you get in a really bad situation. At the same time though, it is entirely possible to run and gun or charge through a situation if you want to. Even if you want to do it via non-lethal means, there are tools and stuff which can really help a player recover from being detected and still continuing the mission.
I guess ultimately, the biggest hook for playing the game stealthy is in the scoring system. Each and every mission is rated and ranked like in the demo, and since missions are relatively short compared to beating an entire MGS game to get a rank, this creates a more immediate reflection in the player to want to improve if you get a poor ranking because of alerts. Missions being replayable immediately also mean that players can retry missions over and over until perfecting them if they wish, or just to screw around with different tactics.
Edit: Stop asking me about the story. I will not answer anything about PW's story, cutscenes or plot elements in this thread. When I'm done I'll probably create a story thread to discuss the plot and spoilers and to contain them there. I will probably comment on the quality of the overall story here after I beat it, but not before.
