To be honest, this "secret war" idea is growing on me, but only if it's a prelude to the actual Alien Invasion- Hear me out.
First, I like the idea of phases, not with the concerning time but the Aliens changing objectives.
I say we shelve Crimson Dagger- it's too conspicuous. The Xenonauts should start up when the powers notice alien influences (not that they know it's aliens mind controlling yet) infiltrating the world. From the Alien's point of view it would be good if they simply controlled the world powers from the shadows and didn't have to do the whole invasion thing.
Obviously, the Xenonauts stop that and at this point it's relatively simple stuff, humans vs humans, the player is generally in an advantageous position to get people used to the mechanics, something I think the original Xenonauts lacked.
Then comes the second phase where the Aliens know open conflict is impossible and starts going original Xenonauts scouting missions to try and weaken the defense of Earth. At this point the Xenonauts organization is the most experienced and knows that it's just the tip of the ice berg. But the world powers do not and are reluctant to invest in the Xenonauts instead of their own (barely holding) conventional forces. Boom- that's the funding mechanic.
In the end the Xenonauts are what ultimately saves the Earth because they've spent most of their budget researching the aliens instead of simply slugging it out with F16s.
That's my 2 cents. Start of human vs human then ramp it up to Xenonauts vs Aliens.
