SS might be the wrong project for him. Only Harley has any real character to her. the rest are awful and their comic-book personalities aren't exactly fun or engaging.
Rocket, Peter and Drax had a certain natural charm, in the source material, that Gunn spun into gold, but what's there to work with in SS?
Maybe he could have done Flash or even Shazam (which isn't looking too bad).
It will be interesting, just because the real creative power at Marvel Studios seems to be Kevin Feige and the production team, rather than the individual directors. Gunn will be under pressure to deliver something close to GOTG; we'll see how well he does without that team he had before.
Or, like Joss Whedon walking away from Batgirl, he might just quit while he still has respect.