Except choice DOES matter. Where are you getting this "there are 2" options from? Are you talking about in a single mission?
Choice matters ALL OVER the game. Choose one option with certain people and/or in certain missions, and that both opens up and cuts off options following that. The game has multiple ending based on what you choose to do throughout it.
Choice DOES matter. Perhaps not as much as YOU would like it to. But that's on you and your expectations.
Have you played the game to it's end?
You are often given choices, yes, but they are merely illusion. The consequences of these are exactly the same in the vast,
vast majority of quests. Furthermore, these consequences have little to no consequences.
---Spoilers ahead---
Here is one example, Cloud 9, when you have to go get Evelyn. You get there, meet with a doll and you can have a deep conversation with that doll. Whether you do or don't has no effect. Then you wake the doll up to ask about Evelyn and you can choose between 3 choices:
- Ask politely for info
- Threaten for info
- Pay for info
All three choices will give you 2 lines of dialogue reacting to your choice and then you immediately get the exact same lines with the exact results and to the VIP section you go. Literally no consequences.
Let's take a quest with a choice that actually affect changes - getting the flathead.
You can either side with Militec or you can side with Maelstrom against Militech. You can directly see the effect of your choice because you'll fight a different faction depending on your choice. It'll even change who you meet when you exit the building. That's where the game shines BECAUSE YOUR CHOICES CHANGES NOTHING AGAIN.
No matter who you sided with and who meets you outside, everyone is happy and here is your flathead. No consequences whatsoever. The game is RIDDLED with these fake choices.
---End of spoilers---
The only choice that changes anything meaningful is at the point of no return and besides 6 different endings, it has no effect on the game or the world.
EDIT: Let me add, the only real choice in the game is whether you do or not a side quest.