Rebel Flesh was WAY better than Curse of the Black Spot.
Anyway. On the Auton theory: the people working with the Flesh (that's what it was called, right?) are humans, right? So that would mean this is the future. But given that we've seen the Autons as far back as the Roman Empire, could their origin occur in the future? Do they have access to time travel?
I'm sure there's a wiki somewhere that's got a list of the Doctor Who races who have time travel technology, but off the top of my head:
Time Lords are the only ones who can really use it effectively. They're the only ones who have TARDISes. Given that there's now only one Time Lord and one TARDIS -- and it's not particularly reliable -- it is probably safe to say that nobody really has the ability to travel anywhere they want in space and time anymore.
Daleks have access to time travel to, but as far as we've seen it's far more limited and unreliable than the Time Lord version. We've seen them take emergency hops through time, and also whatever the fuck happened in The Stolen Earth, but the specifics of the Time War are still unclear.
And Jack's from the future. I forget whether he was an actual time cop or was just impersonating one, but either way that implies that at some point in the future there are human time cops, though if I had to guess I'd say the time cops are probably a coalition consisting of a number of different galactic races.
The Weeping Angels can send people back in time but can't travel through time themselves, or they wouldn't have wanted the TARDIS.
The Cybermen have been sent back in time on more than one occasion (and the ones we've seen on the series to date traveled here from a parallel universe) but so far as I know they don't have time-travel technology themselves.