so I'm a slow learner

Sandra's arc in Atlas. Apparently what you say to the hero matters, and changes whether he helps your or fights you later. I know the first time I did it he attacked me. When I've been doing it recently I must always have chosen the helpful way.

So they can make at least dialog selection have a real impact on a mission.

Is this being used elsewhere and I haven't paid attention to that either?

I take it you haven't done much Praetorian (GR) content?

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The first redside SSA has this, and some of the new DA content, among others.

Going Rogue/Praetoria/Issue 18 really introduced this into the game in conjunction with the alignment system. The whole idea of how your actions could influence your character's fate (a mechanic of which I am quite fond). It hasn't seen much other use red or blue side up to now.

According to your name, you are a VIP, so you should have access to Praetoria. If you like this mechanic I suggest heading over there and running through a bunch of those arcs.

I've done some of Praetoria but only with 2 characters and they chose different paths

so I know that you can choose different paths, but only doing the arcs once I could not tell if they had different effects depending on what you chose.

I should do Praetoria all the way to 20 sometime

In the Galaxy tutorial, if you go villain then talk to Fire Wire or Dr. Geist there, they will remember the conversation later in Mercy Island. I don't think it has any substantial effect, though.

The dialog you get during Mender Ramiel's arc changes depending on what badges you have.

There are also certain arcs where if you have done X contacts arc already, you can phone them up and request for assistance in Ys arc.

Talos Island has this for example