While I haven't read through the whole thing (it's 38 pages, for crying out loud), I have done some good skim reading and got a pretty good idea of what this campaign system is like.
My immediate impression is that I don't like the way this system works. It's basically just the BFG campaign system with the Epic 40k and WH40k systems nailed on. I'm not saying that the Campaign system is bad, it's just not what I want to do with a campaign system. I want to put more weight on the strategy part, not just the 40k and BFG tactics. I didn't see anything about logistics, and missions are usually rolled randomly, which takes away a lot of the strategy from the campaign. For example, with this system you don't have to worry about whether or not it would be wise to commit your forces in a raid or sabotage mission, or a full frontal assault.
I'm also very concerned with the strategic planetary campaigns, where you fight for control of supply routes, airports and starports, city walls, and so on. That's the cool part for me, and absolutely vital when you want to design an inspiring scenario.
For example, you could have a scenario where Space Marines and Imperial Guard are trying to evacuate the Adeptus Terra priesthood from a world invaded by orks. The Imperial player(s) would have to take advantage of the ork player's weak spots, doing everything possible to slow the advance of his largest detachments, trying to gain access to railroads or docks, and finally making the break for the space port. After getting offworld, you have the BFG convoy scenario, where the Imperial transports are trying to break through the ork lines.
Stuff like this just isn't possible with that system. And that's what I'm looking for.
One merit that this campaign system does have, however, is simplicity. Too simple for me though.
PS: And when did anyone in the Warhammer 40,000 universe start taking prisoners!?