I think the issue with picking a side is going to be that both sides have a good point. The fact that the information given to both sides is different means that both sides are generally correct.
In container city, the player is told that Security are going in to secure a dirty bomb that the resistance are making. Its easy to support this mission, and if this were the case it would be hard to support the resistance.
The Resistance are told that they need to protect a vaccine from the securty, who are going to try to take it even though the resistance developed it and need it more. If this is the truth, than its very easy to agree with the resistance, and hard to defend the security actions.
The missions are black and white, but both sides are told information that puts them on the moral high ground. Either both sides are going to be shown to be lying, or neither side is.
That being said, I personally support the security ideology more, they are just trying to protect the ark, and are doing what they have to. I cant support the leader’s choices, but that’s not the fault of the police.
I have trouble putting myself in the mindset of an armed rebellion. If you’re alive, its hard to complain about the people who are keeping you alive, and even worse to demand more at gunpoint. I’m sure that SD will do a fine job of storytelling such that less drastic options just weren’t available anymore, but I still don’t like the ideology.