Well, maybe I'm doing it a disservice, but I honestly feel it was a lot more 1 dimensional than that. I suspect player opposition was a surprise, but even if it was considered, then as you rightly say, there was no way to express that opposition in game, meaning that the outcome was still deterministic, and I simply dont see how we could have ever influenced the galaxy/game. Influencing meta, to me, is an entirely different thing, which does not fall under the remit of influencing the game/galaxy.
Of course giving us an opposition option would have been artificial, but it is a game, and how could FD code the ability for us to influence the galaxy, without giving us options? Without options, it is a traditional, linear narrative, even if it is a lot more protracted than most games.
To be fair, I did enjoy being given the ammunition to rant on the forums, in a pseudo role playing capacity about the evil of Aegis, but did that really have any impact on anybody/anything? I dont think so.
As
@Jorki Rasalas pointed out before me, this story will inevitably lead to the bugs going home to get reinforcements and launching a full scale attack on humanity. It hasn't happened in the time frame I originally expected, but that's probably because they are building up hostilities slowly, ready for the 2020 FPS release. Again, the anticipation of that release, to me, means that the story is pre-determined and we cannot influence it.
So another take on your point about cake vs eating cake would be.....I personally feel that either a) players should be genuinely able to influence the narrative or b) the narrative is linear, in which case it should be stronger than what we saw with Enclave. Just my honest opinion.
Having said this, I have been pleasantly surprised that Galnet fluff going away has already lead to slightly more in game narrative/interaction in the form of a return to weekly community goals, in addition to the IIs. This gives me some hope for the "major upcoming narrative " that we were promised. I guess I just hope that this major narrative is not JUST pew pew and has some intrigue/mystery included.