If you watch the video, you'll realize you can only use mark and execute by playing with stealth. I think this mark and execute is also neccesary to advance certain difficult parts of the game.
They also wanted to make sam more like a real person. If a person is discovered, they're not just going to stand there. The person will make their best effort to survive and escape however and wherever they can.
It's closer to real life where not everything is cut and dry, not everything will go as planned. Things will go wrong and now they allow sam to improvise. Think on your feet, you're outnumbered and have inferior weaponry in a foreign environment. Still you have a particular set of skills to get you out of there and possibly still complete your objective.
Ubisoft montreal have given us the luxury of reaction. When our stealth fails, we don't automatically react game over. We simply react, get the fuck out of there and immediately do whatever it takes to reestablish the advantage of stealth. Just because you were discovered it doesn't mean you can't just as easily dissappear.
