I had this exact situation recently headed AKL-LA. Economy. A very large broad shouldered man who spoke little english seated in the middle between me and another young lady.
As it was a large plane there was plenty of time for me to get to the galley to ask the CSM if anything could be done. His elbows were protruding into my ribs and I wasn't going to spend 14 hours like that. (not that it matters, but I also suffer from a bad back and the contortion I had to be in to not have my ribs dug into was painful). She promptly looked around and said "just sit here for take off and we will sort it out after". So I sat down in another seat, and was promptly yelled at by another passenger for taking his "sky bed" thing (Air NZ). So I apologised, and went back to the CSM who basically said it was full and to sit down and they'll sort it out after takeoff.
Turns out, the other girls boyfriend got an upgrade, she didn't. Her boyfriend came back to economy and the large middle seat fellow got a free upgrade. The CSM gave us all champagne before take off for the whole situation. All in all, an OK outcome, they did the best they could and luckily for me this girls boyfriend was slight.
I would hope a similar outcome in the future and I would not hesitate to raise the issue on board with staff. An hours flight? Maybe I wont bother. Anything much more and I will - I need to be fit to travel otherwise what's the point!