Their are a few quotes out there suggesting that Snyder was willing to proceed with a proper sequel to MoS and was then "forced" to go along with WB's plan. That doesn't strike me as a creative decision made well in advance and suggest that Snyder was at least carrying the wish to direct a proper sequel and not a crossover film until a few months ago.
And as for BO numbers well, you have Robinov's stance. He was expecting MoS to be WB's highest grossing film ever.
I don't think why it would be more logical to think WB planned along ago to have Batman in the sequel, that's exactly where I don't follow your reasonning (and I could ask you in return what proves that WB had a WF movie planned all along, that wouldn't be very interesting don't you think ?). And I don't buy the "Batman featured in the Superman film" thingie either. Everything so far points to a team-up film. You just don't hire a 2 time Oscar winner acclaimed director, force him to drop all his current projects for a cameo in a Superman movie.
Honestly I think WB entertained until very recently 2 options, a strict sequel or a team up film and they opted with the latter when MoS failed to perform on par with their expectations. And I don't think it's a bad decision all in all, I even think it makes a lot of sense business wise, especially if they wanted to release a follow-up to MoS during the very competitive summer 2015. It'll even give them some ground to expect 1b+ from their movie. But it's a business decision more than anything, warranted by financial considerations and rushed because they were constantly outdone by competition for the past 4 years or so when it comes to comic book movies and because they are looking for a franchise able to deliver substantial return on investments on regular basis now that they are done with Harry Potter films. And I just can't buy the idea of MoS' numbers not playing a major role in a business decision.