He in no subtle words complained about "recalcitrant execs" refusing to let female characters to be featured in the movies as they "don't sell toys". Later, it was revealed that Ike Perlmutter held that same belief. He was also talking about how there was a "pressure on him" to have AoU outdo TA, which it didn't. If Snyder is indeed asked to step into a purely exec role for JL, then Whedon will be one of the likely people WB will look at. Only this time, Whedon will be at a better place to negotiate his own terms and conditions.
And I doubt he would want to work on "poor men's X-Men". He may actually get an opportunity at the real thing if Singer wants to take a break after Apocalypse or if Fox have something more in mind for their XCU.