I too was wondering if we would ever see a real male companion again. I agree that Captain Jack and Mickey were just, sort of hitchhikers in a way, not real what I would call companions.
As to sorting out how things that have come before being effected by what is happening in the new series, that's one of the things I love most about time travel stories.
It may be that they came up with "The Time War" to explain away some of those things that they weren't necessarily going to follow through on from the original.
For example, The Doctor is now the only Time Lord in existence. Well, at least until the writers say otherwise. But, even so, before all the other Time Lords were wiped out, certainly they went to places and times were the Doctor has been going too.
Surely he should have run into a few Time Lords in Pompeii on volcano day. But, because of the Time War the rules have changed. He wont be bumping into any Time Lords because after the Time War, all that was time locked. Sealed off. So, the version of himself brought back to be a part of his trial may now never exist because the possible future that existed at that time, no longer does. (You realize Im just full of Jadoon doo doo, and have spent way to much time watching a whole bunch of Sci-fi over the years, right?)
Just one more thing though. Dalek Caan has shown that what was thought to be sealed off and locked away may not be as secured as the Doctor might think. Caan was somehow able to travel back into the time war and bring Davros and therefore the Daleks out of it. So, perhaps there is some hope that the lonely Time Lord wont always remain so.
