@karajorma
I wouldn't be surprised if there were hooks in there for alternate paths. What I'm referring to was mostly about what the mission tells you and what you perceive you are allowed to do. The perception of what you are allowed to do combined with what you are actually allowed to do is what some of us in academia believe gives that feeling of agency. If a game incorporates the player not doing what they are supposed to, that's even better, especially if it doesn't tell the player they have alternatives.
That specific anecdote was included mostly out of it being really fresh in my head while I was writing, partially because of how many times I'd failed

. I'm also trying to get my point across to people who've never heard of the retail game, let alone any of the work done here.
@Scott
I'd agree with you that FreeSpace's mechanics are on the simple side, which is to its benefit. FreeSpace also has a large amount of depth to its mechanics mainly through the systems they build, which have been improved upon by the community's creativity.
I'm not sure if I agree that FreeSpace having more mechanics would inherently alter its gameplay and story relationship. One of the most important reasons for FreeSpace's feeling of agency is how your available interactions, with a few exceptions, are the same regardless of the mission, just the consequences for those actions change. This includes those stealth missions where you still have weapons access and can get involved in combat.