1. Yeah it's NINJA SKILLS of hitting the enemy in the throat or the eye, instead of just firing in the centre of mass. Or something like that. It's a simulation, but obviously not 1:1 simulation. But ninja weapons do add something unique gameplay wise, so they'll stay.
2. The throwing penalty on the heavy armor is mostly because of grenades and bows, not knives.
3. You're welcome to find any mod which has more faction variety. It's not my ill-will but I only have a single life.
4. It has been discussed. It's a good idea but way impossible in this engine.
5. Do you really think you could simply 'take out' the Eurosyndicate? Lol. But yes, in principle it does make sense (but again, way impossible).