First of all, I had a good time, and thought that the missions this time were better than the ones I'd seen in the past. Bravo for finding and picking them! There's the issue of kill points, where I agree with the other commenters, but fundamentally, strong rule set. I LOVED having more than one goal.
So, about kill points, I believe that every game I won, I won on kill points, and every game I lost, I lost on kill points. That's the issue. Let's say you have a deep striking squad, and the cards have given you an objective in enemy territory. In a pure maelstrom mission, you go for it, but in a mission combined with kill points, losing the unit would lose you the point you just gained, and you're often better off ignoring your maelstrom objectives. I don't want to be calculating everything all game long in terms of the kill points.
I do have a couple of specific suggestions that might work.
To lessen the impact of kill points, you could halve their impact, or have them only count in 1-2 missions. Kill points in WH40K has been reduced to a single eternal war mission, after all.
Also, the maelstrom edits were confusing. I have a deck of maelstrom mission cards, and they say things like one point for killing one unit, while the chart of edits said 2 points for killing 3 units. I *think* I always remembered to use the edited rules. And what happens when you run out of objectives? Using maelstrom cards as-is would make things a lot easier. Or give us simpler edits.
But again, great tournament, and I agree with fiesta that the missions were more balanced, and with MikeK very very much about the challenge and diversity! It was nice to not have every mission start with the same deployment, too.