I know that the official explanation seems to be that the Genesis Ark is a prison, but that really doesn't seem to make much sense.
*Flashback Scene*
Timelord Tom-'Hey we captured a whole bunch of nasty Dalek chaps trying to exterminate us. What should we do, kill them?'
Timelord Harry-'Nah, that wouldn't be sporting. Instead lets build an incredibly advanced but lockless prison and chuck them in. Better not disarm them either, you never know when it'll come in handy for them to escape and go on an exterminating rampage.'
Timelord Tom-'Brilliant!'
It might be wishful thinking on my part, but I hope the Genesis Ark was actually a Timelord attempt to preserve some of their race. It would seem to be a good lifeboat, and once put in the void would let them escape whatever the Daleks did to completely remove the Timelords from space/time. It's quite possible the voidship was also Timelord technology. That way the Timelords can return in the series via a second Genesis Ark filled with Timelords.