Been reading on some posts here talking about having McGann instead of Hurt. This could have actually been a great idea. Having a doctor as the actual villain, would be great. Would show us that the time war was so catastrophic, a romantic, young, and polite man would become bitter and do some things so bad, all future doctors look down on him. I think that would have had much more of an impact, plus McGann would have played an outstanding evil doctor. He could wear his 2010 redesigned outfit. That would have been great, plus we'd have gotten our fill of the classic series.
As for old companions, I think Jamie should return for one episode outside the 50th. The doctor and his assistant at the time would go to Scotland somewhere in the lifespan of Jamie's, and the Doctor would bump into him as an old man, but of course after the events of the War Games, Jamie has no memory of the doctor, plus he's regenerated like ten times since their last meeting. The episode would go with the doctor becoming a bit emotional in the episode, and Jamie isn't the nicest guy to him as some war has made him a bit more bitter. But a bit like the Master in Utopia, he starts to get flashbacks of his time in the TARDIS (plus we get to see old scenes from the sixties!!!!!). The episode would be a little bit like that Van Gogh one, you know, more emotional and such. Eventually, some alien or threat (maybe a full historical episode?) end up with Jamie getting shot or something, and he dies in the Doctors arms, and in the last moments remembers the Doctor and everything. Then Jamie dies in the Doctors arms and the doctor starts crying. So yeah, basically it would be a very emotional episode and a good nod to the classic series.
Would have been great with Matt Smith due to the fact he's so alike to the second Doctor, but unfortunately that won't happen. But it could work with Capaldi too.