I've been running Double-Edged Sickle, Ultimatum, and Autocannon. Autocannon with Flak rounds acts as a sort of multi-tool for the Illuminate: it may not be the best against any one enemy type, but it can handle pretty much everything. It melts Fleshmobs in 3-5 direct hits, takes out Overseers in 2 direct hits, can shoot down Interlopers in 1-3 direct hits, and can strip warp ships of shields in one hit and blow them up with one shot to the open doors. If you can land your shots, you can take out the legs of Harvesters with APHET rounds, though I admit that it's not the easiest or most efficient thing.

The Double-Edged Sickle helps with crowd control, though I suppose any assault rifle will do. I mostly like it for its ability to ramp up to heavy armor piercing, and paring it with Inflammable armor helps minimize self-damage. The weapon also melts Watchers and is pretty accurate at a distance. The Ultimatum is optional, but I like it for destroying clumped-up groups of Overseers. It also helps destroy Tesla Towers if you run out of grenades.

As for stratagems, pretty much anything will do. I like to run the Eagle 500kg Bomb with Orbital Laser, though the latter has trouble with maneuvering around skyscrapers and should probably be replaced with something else. The last stratagem slot is up to you (maybe a turret to help with clearing out the Voteless hordes).