Okay let me fill you in with some facts mixed in with my own opinion
1. Another stand-alone Superman film would've been fine yes...but a Superman/Batman film puts asses in the seats and lets DC/WB also move forward on their own DC Cinematic Universe plans. It's a win-win situation versus taking another risk like they did with GL and crashed and burned. They want nothing but momentum and sure things at this point as they gear up for Justice League,can't take another big risk so soon and we all know that making this Man of Steel sequel a Superman/Batman film takes care of everything they want to accomplish in the near future.
2.Nolan's Batman is still a tad fresh in folks minds but this Superman/Batman film won't be arriving until the summer of 2015,that's not too bad..lot of people will know nothing about the movie until 2015 rolls around. Plus many aren't that wary of it in the first place and aren't that attached to the Nolan verse to disregard something new. Bale was solid but Nolan's script and directing carried those films not him.
3.Yes there's more to DC than Superman and Batman and WB knows that very well,however like I said in #1 they also can't afford to take a big risk just yet after taking a hit with the GL film. They're also dead set on gaining momentum and making good decisions toward the JL film. The confirmed live-action film slate for DC/WB is "SUPERMAN/BATMAN" July 17th,2015, "FLASH" in 2016 and "JUSTICE LEAGUE" in 2017. This was all said at Comic-Con this summer which means we'll have the Superman,Affleck's Batman and The Flash established by the time JL rolls around with Wonder Woman and the new GL to be introduced
When I said 'introduce other characters into the Man of Steel universe' it doesn't necessarily have to be a full on co-starring role or their on standalone movie (look at how Black Widow was introduced in 'Iron Man 2' or how Hawkeye was in 'Thor'). If done in a similar fashion and Superman was basically still the star and carrying his own movie...it would still put asses in the seats. As well as introducing other important JL characters without taking too big of a risk.
Because the risk is gonna be the collaboration movies themselves (which the supposed 'MoS' sequel is gonna be). Think about it, if the Avengers came out and was nothing but hot garbage...do you think DC/WB would be so antsy to go and, all of a sudden, get their super heroes together on the big screen?
The Avengers was a risk. Part of the reason it paid off for them is because, Marvel laid out a blueprint on how they wanted to go about doing it (other reasons being the script and good cast). Yeah, DC/WB may be planning to do standalone films for their lesser known heroes in the years to come like you said, but as far as bringing their characters together on screen...I'm a little more skeptical than optimistic.
Part of the reason being is, also like you mentioned, is because their too into falling on Batman and Superman (more so Batman) for momentum and putting 'asses in the seats.' Somewhat a shame....all the awesome characters in DC Comics and the only two they don't think of as 'risks' when it comes to live action movies is Bruce Wayne/Batman and Clark Kent/Superman.