I've just met Samuel L Jackson at the US Inauguration, and I asked him about this. He only said "I hope so." I hope so too!
He's holding out for the best deal he can, no different than any of us would likely do. The problem is dragging it into public like this can backfire badly.
Hopefully, in the end, they'll be able to work something out and Jackson will be wearing the eyepatch once again. If worse came the worse, they could go with the idea people have been kicking around and say that Jackson wasn't the real Nick Fury and was only a decoy. On another note, George Clooney has always been my choice for a 616 Fury.
Well now I wouldn't go that far. While I don't think anybody could deny Robert Downey Jr. was born to play Tony Stark (similarities in personality, as well as vices), Ultimate Fury was actually modeled around Samuel L. Jackson. That character also has many similarities to the original Nick Fury, but if you really look at them closely, they are different characters with the same name. It would be closer to say Sam Jackson was born to inspire a reimaging of Nick Fury. That said, I agree it would be a huge mistake to introduce Jackson as Nick Fury (in arguably the BEST super hero movie EVER) and then try to fill the role later with any other actor. Unless, as has been said before, they explain that the previous Fury was a decoy and the real one is actually (insert actor here). But even then you know the fandom (including me) is gonna be pissed if he doesn't look like 616. And then you have to explain the whole alternate universes thing and I don't know if they really want to get into that yet. I dunno. Really hope they do end up going with Jackson.
Honestly, they can get Dennis Haysbert who plays Jonas Blane on the CBS show The Unit. He also does the Allstate commercials. He is pretty badass and most likely a better suit for Nick Fury.