I can't believe I've only just found this. This is awesome, great work! I won't be getting much done for the next week or so.
I've only played the first mission, just now, but there's a couple problems I found.
When I looked at the second mission just to see the layout the music that plays when you choose your equipment didn't stop, so there were two tracks playing over each other.
After his first turn the dreadnought wasn't able to use one of his heavy weapons but I hadn't wounded it. Then on the next turn I killed it by shooting and scoring four. So I think it only has an armour value of two.
After moving or attacking with a marine you can't select a different marine and go back to use the other action later. You could definitely do that in the official computer game and I think in the board game as well.
I wasted the medi kit in the first turn by clicking on it by mistake and started again. Maybe a confirm box for equipment and orders.
I miss the 3-D animations when I move and attack, but I used to wish they were skippable to speed things up so maybe I'm just never happy.
With auto rerolling you miss out on the choices to either stick with a roll that kills something or gamble and go for a higher score.
Order cards affect the commander as well. They didn't in the official computer game.
I had a quick look at the mission creator (lovely addition) but I couldn't place a docking claw anywhere. It just stayed red. Maybe I was doing something wrong. I only had a quick play with editor.
I think marines should be able to exit the mission on any of the docking claws. I know it's not like that in the actual games but it would speed up the most tedius part.
I think there should also be an option for the chapters to have a random order of play every turn so that the blood angles aren't unfairly favoured and the ultramarines aren't always at a disadvantage.