I played it, and that was pretty poor in execution like you said. My thinking is very different though. I meant instead of starting with whatever the name of the guy was in Killzone 2/3, and then moving in an uninspired direction with Shadow Fall, they should've planned a real story arc, and thrown us in there with some kind of half-Helghast soldier in Killzone 2. Imagine if you're a super soldier Helghast that can jump further. That one ability alone could allow the gameplay to change in certain ways.
You could begin on the Helghast side, before transitioning to ISA side in Killzone 2, and you have plenty of conflict to explore there internally. It's just a better position to start from in terms of character conflict, and since Killzone is all about the Helghast, it's not a bad idea to use that as a base for your protagonist either. And if you're a bit enhanced in terms of ability, it opens up a bit more in regards to gameplay, rather than keeping to the standard mechanics which are found in every FPS.
This is really a case of two very different visions really, so it's obvious why what I want didn't happen. It'd mean changing the game entirely in some ways. I still think it would've been better. Super soldier is generic, sure. But the backstory of the world, and making that protagonist a half-Helghast, allows you to move away from that.
In an ideal world, I'd honestly make it a third person shooter starring a half-Helghast ninja who is adept with both knives, and guns, and I'd add some stealth elements. Like, what's in my mind right now, is so good and I'd probably love that game. Never going to happen though.