Okay so I used to be pretty into the Killzone lore but it's been a while so forgive me if I mess up as I try to address those scenes. Some of these thoughts are from what I have heard others say, so :p

Scene 1: The Helghast are using a nuke on their own citry in order to strike a devastating blow to the ISA forces. I believe that particular nuke is the one they stole from the ISA in Killzone: Liberation (The PSP game, never played it). Radec executed the soldier because he knew what the intention for that nuke was and Radec didn't want that information getting out. I believe the Helghast blamed the nuking of their city on the ISA as to stir up a deeper resentment of the ISA from the Helghast people. They couldn't let anyone find out that the Helghast military was nuking its own city, so that meant tieing up any loose ends. If I remember correctly the soldier salutes before accepting the execution. The Helghast soldiers are seriously loyal to the cause/well trained.

Scene 2: This one is a bit more speculation based. Some people believe that the Scholar Visari you are looking through in the intro is actually a body double. When the daugher reaches out her hand she believes she is doing so to her father, but quickly realizes it isn't him so she pulls back. Another point of support for this theory is that yeah, as you mentioned the eye colors from different cutscenes (can't remember which games) are different. In one cutscene the eyes are brown or something and in another they are green/blue. Some people believe this to be intentional while others believe this to be an oversight by GG.

Fun stuff. Some speculate that the "welcome back sir" at the end of the third game is referring to Visari. Others believe the shadow of the figure to resemble Stalh. Who knows, they probably purposely left this open so they could have more freedom with Killzone 4.

Hope I helped a little :]

Its Visari, without a doubt Visari's eyes are red at the starting intro of KZ2 , but at the end of KZ2 there green, and note at the start of KZ2 how Visari's daughter pulls her hand away suprised when he kisses her hand, Its a body double.

KZ4 will still be played as the ISA but I think they'll introduce a new enemy. Then while humans are busy defending against a new threat the weakened Helgan can do some serious damage.

thats exactly what I thought! thanks, it seemed that everyone kept ignoring that :D

Scene 1 : ok that makes sense. It just seems special as stahl is also on the picture, so Stahl/Radec/Visari are all informed about the plan to change visari with a double. So radec sacrifices himself so that the ISA think that its the real Visari.

Why isn't orloc introduced into the plan? If he is Visaris right hand, he definately should have been.

aaaaaaah I really dig that they did that and kept unanswered questions, LOVE it!

I hope its visari, that comes out of the capsule because Stahl would be so...standard.

(just thought about HOW GREAT of a plan that was, telling the Helghast that Visari, their savior is dead and now they have to fight the ISA, sheeesh, of course they are going rampant!!!)