I don't think he was that bad defensively today as he had quite a difficult task, given Stoke's willingness to cross from deep it makes it very difficult to play against them from the wide positions because if you press the ball to stop them from crossing the ball you'll leave space in behind which was potentially a problem because they overloaded that side.
A few times I saw him caught between pressing the ball to stop the cross and staying as part of the back four, Johnson had a similar problem which was arguably worse because Arnautovic is equally good at crossing the ball with both feet and can go past players.
In possession he's never going to offer much going forward, he is as good with the ball as the options that are available to him, this seems really weird to me because from what I remember of him at Porto his ability going forward was one of the things that really stood out.
With all that said Flanagan will still walk back into the team.