Or maybe Eccleston like myself and many others are fed up with all these giant plot twists and complicated shit that goes on. And with Moffat, he always marks an occasion with some stupid "altering the universe with complicated plot twists" crap that Eccleston may not like, and I get the feeling he's a bit more down to Earth with the show.
Yes, that's it. Clearly. Christopher Eccleston, acclaimed actor of stage and screen, declined to shoot a Doctor Who anniversary episode because he's upset we never found out why the 52nd Century Anglican Church allied itself with the Order of the Headless Monks and the Silence.

apparently it keeps him awake at night!
Yeah, I think Moffat also treated John Barrowman with crap too. I heard rumours that he was asked to come back for series 6 (probably to join Amy Rory and River in episodes 1 & 2) but turned it down because he had scheduling conflicts, so couldn't' do it, and after that Moffat's in a sulk and that's probably why he's not in the 50th. So from what I've heard of how Moffat treated Eccleston and Barrowman, no wonder Eccleston declined. From what I've heard, Moffat sounds like an impatient git who writes only for himself.
Or maybe Eccleston like myself and many others are fed up with all these giant plot twists and complicated shit that goes on. And with Moffat, he always marks an occasion with some stupid "altering the universe with complicated plot twists" crap that Eccleston may not like, and I get the feeling he's a bit more down to Earth with the show.
Or maybe you're confusing your own feelings about Moffatt with Eccleston's own, unknown-to-us, reasons for not appearing in the episode.
You know I think you might be on to something there...
As for Moffat, he can come off a bit smug and arrogant, but I think that comes with the territory, RTD could also. There's very few reports come out of people being unable to work with him however (former executive producer not withstanding) the main issue people have with him is how long he takes to write his episodes! But having read interviews with Gaiman where he explained how much work just writing one episode entailed it may be that Moffat isn't that unusual in this respect, and that maybe RTD was just a bit of a (in the nicest possible terms) freak in terms of how quickly he could turn scripts around
Eccelston at least talked to Moffat which he didn't have to do. It may be that he wasn't interested but was being polite, it may be that it was a situation like Nimoy with Generations, he didn't see the point of coming back just for a few minutes of screen time.
Or maybe Moffat spat on him, called him a gruff Northern bastard and told him to eff off