Okay, I finished replaying it. Bummed to see that both Mission 3 and 4 are truncated even on first play. The flyin to the Guardian with the tense com chatter was one of my favorite parts, and now it's gone; so is the intense cinematic battle around the Guardian.
I don't really understand your decisions here. You clearly have the missions set up in clean, distinct stages. All the parts that are annoying to do over and over again on a replay are separated from the combat sections by a jump. Your missions seem to ALREADY have clear checkpoints; you're just not letting the player use them.
Why not, after completing the second stage of mission 3 and 4, simply unlock the option for the player to go straight to the third stage on replays? This wouldn't even require fancy scripting, aside from giving the player the choice.
This would let you preserve the great initial presentation of the minefield/waypoint sequences AND the intensity of the combat.
I haven't cranked up the difficulty all the way to the top yet, but I did find the Raiders a little toothless this time around, even on Advanced. They can barely hurt you in 1v1 circling combat.
I feel the wrong message was taken from the feedback here. Hard combat can be really fun! The problem is not dying in combat, it's having to replay tons of downtime—sequences the player has already mastered—to get back to the skill intensive part.
I love so much about this campaign and hope we see a lot more. I really hope you will consider restoring the old missions but simply letting the player cut directly to the combat sequences once they've reached them for the first time. If you want help I feel like I could do this in a day or two.