If Eccleston turned something down I think it was probably doing a regeneration scene from "time war doctor" into 9. A "hidden" regeneration fits a lot of things that have gone on since 2005.
Now we've seen the McGann mini-episode it makes sense that 8 was trying not to get involved in the war, even up to the point where he was sticking his head in the sand about it. He still wanted to do his normal thing of going travelling with a companion, but by then the war had affected so much of the universe that no one even wanted to be rescued by a time lord because of it all. In any case, there wouldn't be much of the universe left to explore by that stage either by the looks of it. It must have been very sad for him. After his chat with the Sisters of Karn he decides he does have to do something about it, so takes their advice and chooses a 'type' for his next regeneration that will be able to knock both sets of heads together- Time lords and Daleks, for the greater good of the universe. He pretty much goes into that regen already regretting what he's going to have to do. And afterwards ( as we see from 2005 onwards in 9 and 10's portrayal) he's still torn up about it and trying to forget.
He probably doesn't remember everything about it either. And since it looks like there may be some involvement with other doctors too, (as seen in the trailers for the 50th anniversary), this all fits as well. Way back to the first multi-doctor stories there has always been some 'fuzzy memory syndrome' going on around meeting his past selves etc. ( I like to think that there are bits of a time lords brain that aren't really there, or are half there and half not sometimes but not all the time, and don't get fully formed in his brain until all of them that are meeting each other have experienced it. That's why sometimes he remembers little bits of meeting himself and sometimes doesn't until after it has happened to all of them. Before, there was also the time lords around, when they were in a more benevolent mood pre time war, who would help out with erasing memories etc. too.)
So we have a time war- a war the doctor was involved in, which he didn't really want to do. He did , in the end, allow himself to become involved, but at the cost wiping what happened in his memory, part by choice and part by what happened. So he wants to forget about it, and also doesn't remember all of it either. the John Hurt 'war doctor' does still exist though, and might actually be a bit pissed off that he's shunned so much, because he was the one who did what had to be done, and none of the others want to know. they'd probably not be there if it wasn't for him, and neither would most of the universe.
To be shut out of his own memories for taking the responsibility that no one else wanted is a bit of a downer to say the least. Especially if it turns out that some of his other incarnations actually helped him ( No- not a spoiler, it's just a possibility from the trailers).
Anyway- I ended up rambling a lot there
I would have loved to see McGann more, he certainly deserves it, but I do think the plan was always, or evolved out of an idea to have, some kind of forgotten doctor that did most of the 'time war stuff'. BUT- you know there's plenty of possibility for more mini-sodes or something.
Even - the next time they want to have a doctor-lite episode they could stick him in there. Just imagine at the end of a Peter Capaldi episode some baddie's name is mentioned that McGann met in a radio episode? Peter says " I haven't met them since...."then the episode ends.........THEN no next time trailer, OR a next time trailer which only shows the baddies and not the doctor. Or a little hint that he might be regenerating already, if Peter had a blow to the head or something before talking about all this. And when next week arrives it's Doc 8 on the screen- we see a whole episode with doc 8 and Lucie Miller or something fighting said baddies, and at the end Peter is telling Clara ( or new companion?) "so that's what happened with those guys, anyway I wonder what they want this time..." And then a week later it could either be forgotten about, or we could be seeing Peter fight the same bad guys.
Just a little idea
But I think it would be A-MAZ-ING to see soemthing like that. It gives Peter time off from a heavy filming schedule- which the crew always seem to want to get ( A doctor lite episode as we call it), it gives the fans a huge thing to cheer about. it would be a 'must watch' thing for the whole country if there's a little hint McGann might be appearing. It would probably blow the ratings off the charts.
What I'm getting it is that it's not impossible. Someone just has to write it and Moffat make it happen in the schedule. It doesn't have to involve the 'nightmare' or working out a multi-doctor thing as well.
