It does do a poor job of incentivizing you. The mission variety is severely lacking, and never forces you outside of your comfort zone. You can beat 99% of them with the same approach, and most people will do just that, because why try anything else when you're getting by just sneaking and picking the baddies off? On top of that, the main missions have this arbitrary, yet incredibly annoying rating system that penalizes you for messing around with a good portion of the weaponry. Why would you even want to use a machine gun, if the game is gonna ding you for killing people and alerting guards? Let alone the rest of less than stealthy arsenal.
Most people are gonna play this game like this on their first run, if they want to play it stealthily. Binoculars, mark, mark, mark, sneak, sneak, sneak, tranq, tranq, tranq, with the occasional CQC and interrogation, and pulling out the lethal weapons when they fuck up. In between that, they'll collect shit for the base. Clear area, collect shit, do mission goal, and repeat. Unless you absolutely love the game, most people aren't going to take the time to fuck around with it too much.
Don't get me wrong, I get what you're saying, and I do think the game offers you a ridiculous amount of freedom if you take the time to learn all of it's intricacies. I'm just saying the game doesn't do a good job at making you want to experiment with it. Most just want to beat the missions as directly as possible, and anything after that, is gonna be left for the more hardcore players.
As for the story, and how it's told, meh. Give me my 30 minute cutscenes back, please.