The Doctor called them for help in The War Games and basically gave himself up that way. What I meant to say is that normally, the Timelords don't care enough about their renegades that they would hunt them down.
I don't think the Timelords being there but mainly keeping to themselves is such a difficult concept to grasp.
If that was all there was to it, sure, that'd be fine.
But then we find out that they do things like, arrest people for running away and doing their own thing.
Which makes no sense. Either they don't care or they do; if they care, it would be child's play to catch the Doctor. If they don't, then why bother arresting him, trying him, and exiling him?
That they didn't manage to take all Daleks down with them after all fits the picture.
The Doctor was the one who destroyed (almost) all the Daleks, not the Time Lords.
It does, if the Time Lords are so much more powerful that those forces are a nuisance to them rather than a danger.
Then why need the Doctor fear them? Why is he on the run? Why would they bother arresting him and exiling him, if he's so unimportant?
In the end, they don't need explanation, if the show runners don't want to use them, just don't.
That just makes them an arbitrary plot device.