I'm currently working my way through series 1 of nuWho. And one thing that I've come to realize is Eccleston is a real standout as the Doctor. To me Tennant just overshadowed him when he showed up, so I had kind of forgotten how cool Nine really is. I know it's a longshot, but I'd love to see him come back, just to see how he'd interact with his more siller successors.
In many ways it would be easier to just have old companions show up, because at least then the fact that they've aged poses no problems what so ever. I hope we get to see some older Doctors (heck I want to see all of them) but I'd also love to see a clutch of companions from across the show's history.
I know that this will never happen, but here is my dream for the 50th anniversary. The season première is a generic episode involving the 11th Doctor, when, after saving the day with about 10 minutes remaining, the White Guardian appears and tasks the Doctor with teaming up with his previous selves to combat the Black Guardian. Each of the following 10 episodes, starting with the 10th Doctor and ending with the 1st, will have Matt Smith taking part in an adventure alongside that Doctor and his companion(s) in the style of that Doctor's era. The 1st, 2nd, and 3rd Doctors will have already been killed by the Black Guardian and only their companions (Ian/Susan and Jamie/Zoe and Jo/UNIT) will take part in that episode. That takes up 11 episodes. In the two part finale, the companions are ditched and the 8 Doctors (4 to 11) team up to save all of creation from the Black Guardian.
I'm on board with this myself, I didn't go so far as defining a story, but, I too have envisioned how great I think it would be to have a Series long Arc (bringing in an "Era group" an episode [or 2 groups for a 2 parter?]), culminating in the Anniversary Special I'd be OK with it being either the Series 8 Climax, or even as the first part of a 3 parter (If there's 2 regular episodes after the Anniversary)
Another thing that's occurred to me that I'd like to see is that they should cast David & Michael Troughton and Sean Pertwee - and a surviving descendant of Hartnell - in the anniversary show. Not as The Doctor, or even as anyone related to him, but just in general roles within the episode...
^I've wanted Sam Troughton to show up at some point on Doctor Who ever since I first saw him absolutely steal the show on Robin Hood. I don't care what he plays on Doctor Who. (But if they cast him as yet another member of the royal family of Peladon, I wouldn't object.) Well, in fairness, I do get the impression that some of the commentators are familiar with the classic series, but a lot of them aren't. But there's absolutely nothing wrong with gushing about Matt Smith. (Gushing about David Tennant on the other hand...) But mostly, the only thing I really like about those specials is the realization that Pete from 30 Rock is a Whovian.