@EgoMania
"....The choice is between releasing the pods or blowing up the base because there is time pressure..."
You're only partially correct here because you're remembering the situation incorrectly. What actually takes place is that initially they state that there is no way they could open all the pods before reinforcements arrive. This has nothing to do with your ability to blow up the base as SAM gives you the ability to do so pretty early on.
The Cardinal then offers to automatically open all pods, long as you agree to leave their "holy place" intact. A condition they would not have needed to specify at all if the two were intertwined. They are not.
"...Being able to lie or be deceptive is something that would be more involved than just a choice..."
It's not really. The reason it isn't is for the same reason they didn't have to build a whole new mechanic when they allow you to make impulsive decisions from time to time. Even though you, on some occasions, can choose to just shoot a hostage taker (or at least once you can), hostage takers still try talking to you rather than the game needing to decide if they would based on you killing them before.
Same thing here. Occasionally you could be able to lie and have it not always be an option and I already even explained how it would even make sense to let it affect an event later on if negotiating with the Kett would be an option in a future mission.
But re-vamping the entire system would be overkill and unnecessary.
EDIT:
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@VladVonCastein
Some valid points, but I wasn't looking for this to mirror real life. Real life is too complicated, but in that case and a handful of other missions, it just seems like the option should naturally be there in my opinion.
It's like I accept we're going to have limitations, but sometimes we're unreasonably and or illogically limited. The Moshae rescue is absolutely one of those situations in my opinion.
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@Vellu78
"...In this particular case it's a plot device (has to go one way or the other) so deal with it...."
I am. I am also going to voice my opinion just like you're going to voice yours about not having different kinds of options that you personally feel like are not douche enough for you. Deal with that.