Well, I donno, it kind of does fall into the "mistake" part of Sync/Transcend, in the fact that there's obviously little to no thought put into whether the mission is actually...fun. You could get rid of all the combat in most of the missions and the campaign wouldn't be any worse for it... In fact it might be better, if you don't have to fight off 2-3 random wings of fighters every jump, etc. We'll call it "Transcend Syndrome", where, in the attempt to tell a great story, the gameplay aspect is forgotten, and player interaction is token, thrown in just because there needs to be something for the player to do, which has little to no relevance to the story or anything else.
At this point, I'm rather opposed to the idea of a "novel-esque" mission, unless you have a very good reason of having one. (And if you're wondering if you do have a very good reason, you do not.) There certainly should not be many of them...otherwise you're losing sight of what it means to be a game.
Gameplay and storytelling are intrinsically opposed. One depends on giving player agency to encourage interaction, and the other depends on limiting it to direct the narrative... You should aim to strike a balance, and err on the side of less story more gameplay, IMO, unless you're sure your story is good enough, or you can pull it off. (and even then, you should still consider if your story would or would not be better off in written medium).