First, I still think that the Terminator series ties in nicely (not perfectly, but nicely) with the Matrix series.
Second, I wish there was some way to adress the time paradoxes in the Terminator series. Like John Conner would not have been born if they hadn't gone back in time to save him.
That last one led me to pondering a Doctor Who tie-in, where the Doctor must heal the paradox and save mankind, which without his assistance would be enslaved into cybermen. Originally with freewill, created as an advisory group similar to the Cult of Skaro, leading up to the cult breaking off and creating a fully enslaved cyberman army, that eventually loses to Skynet and is trapped in the Matrix.