Hmm, I would think more of this.
Earth invaded, bad things, lot's of deaths. The culprit is a dark spirit which has managed to escape from the collective subconcious of the (vaguely psi capable) humans. As it was born out of the emotions of terror and hate it wants to destroy all mankind, etc.
The Great Shadow has a problem however, it can't exert much influence. It has managed however to form semi-physical hulls and to house dark spirits in them. These beings are capable of constructing semi-physical buildings and can in addition give up their physical side to become ghosts or give up their ghostly side to become purely physical.
The builders can also evolve into more powerful mixed classes. They do this by tapping into the power of the base. When the base damages humans it takes some of their live energy, this energy is used to repair the base but is also spread to builders.
The physical shadows aren't too interesting, think aliens. The strongest shadow type is physical. Basically these form a simple to play class for the player who likes things simple.
The ghosts are far more complex. Ghosts can fly, but not through walls (the walls are of a material that they can't get through). Smaller ghosts make excellent scouts, they can't do much damage and are easily killed, but a loner going out without a psi is well within their reach.
At higher level ghosts get a very important ability: spatial manipulation. It works like this: one ghost uses some life energy (stolen from humans of course) to gather. Another ghost can then (for free/semi-free) jump (trigger) to him over a certain distance. In addition if a mixed shadow is near a ghost when it triggers it gets triggered too.
In addition the attacks of ghosts increase by level, the highest level ones even have a ranged terror bolt attack.
The mixed shadows have the ability to go invisible (except to psi's) for a short period of time and have additional special attacks (think adv maurader electro attack).
It's worth noticing that shadows don't heal automatically, but only when damaging humans.
The shadows evolve when they eat enough life energy for the Great Shadow to be pleased with them.
After the shadows invaded scientists of a secret research program noticed that those humans who have a strong connection with the unseeable (the psi's) are capable of seeing the ghosts.
During an accident in which nanites spilled onto the head of a strong psi it was discovered that some psi's are capable of interfacing with nanites, forming psiborgs (sorry, couldn't refuse the pun).
Further experimentation revealed that a group of psi's will under combat conditions evolve in three steps. In the first step every psi is alone and there is no binding with nanites. In the second step psi's begin to connect to eachothers minds and to nanites. In the third step the group will have achieved a collective conciousness and full control of nanites.
Now combat trained psi's are capable of turning their gift down so that they can wield weapons. They are still much less vulnerable to ghost attacks as normal people though. Hence it was decided that only psi's can enter the realm of battle.
Unlike the class based shadows the humans progress with upgrades. As all humans are psi's all can act like psi's if they chose the right upgrades. The effective psi's are capable of seeing ghosts and have a small not really effective light gun to shoot at them and (more importantly) point them out to the others. The soldiers have light guns for ghosts (and mixeds, those are vulnerable to both type of guns, but less) and balistic/energy for physicals.
At step 2 soldiers get a kind of psychic map on their hud, showing where about ghosts are, if a psychic is near. At step 3 soldiers see the ghosts if psychics are near.
Psi's can at later levels become doctors (making humans much more mobile than Trem humans) or psi soldiers (capable of shooting with a special anti-ghost gun).
Soldiers get, in addition to the usual cool guns, some nice little upgrades. One of which is the chrono accelerator. This little device allows soldiers to move really quickly in one direction every once in a while. Also humans get hyper boots, allowing high jumping (as a jetpack replacement).
Another big text and another disclaimer

: I also have a few too much things on my hands to get very involved.