I think the real answer has nothing to do with character, power-sets, costumes, iconography, nor any of the other interesting aspects of superhero comics. I think it comes down to the competency of the respective studios and their creative teams.
Prior to Batman Begins, WB was really exploring some serious risks as to the direction of the Batman franchise. After two Schumacher flicks, WB had the whole crisis/opportunity thing going, so they kicked around the idea of swinging for the fences with Batman. Frank Miller and Darren Aronofsky were brought in to develop/direct an untitled Batman project. The arthouse director generated a lot of positive buzz with college kids who hated at least 2/4 if not 4/4 Batman movies, plus the inclusion of Miller strongly suggested a tonally darker, more serious take ala Dark Knight Returns 1986 comic. Ultimately, their concept was too out there including a blue collar Batman and Alfred as a mechanic called Big Al.
The groundwork had been laid for an arthouse direction though – enter Christopher Nolan – who pre-Inception and Prestige, only had small pics like Memento and Insomnia under his belt. Long story short we know how well this creative team worked out – BUT WB was not ready with a cohesive plan ala Marvel/Disney’s build-up to Avengers. Additionally, the Nolan/Goyer built Batman continuity felt too closed from the spectacular and too grounded. In a Chicago-as-Gotham where great pains were taken to explain how a billionaire could glide, one would never believe that “a man can fly.” Neverless, 2006’s Superman Returns was supposed to eventually tie into the Nolan-verse, but Singer’s film was a turd.
Post Batman, the Green Lantern movie was supposed to be fresh start and springboard for a cohesive DCU on film. Also a flop.
Finally, a passable Superman movie was made, and for once WB isn’t tasked with polishing a turd, however, everything is being tacked onto the Superman/Batman movie in the least organically built up way possible – for better or worse.
Look at Marvel’s failures by comparison. Hulk was bad, it was followed with an “Eh” quasi-reboot, which was followed by a recasted Hulk/Banner in Avengers. Then you’ve got ten seconds of Nick Fury tacked onto to an Iron Man flick just in case it’s a hit - it was. Point being, Marvel Studios is at once more fast and loose and better at mapping out a connected film universe. Sam Jackson’s cameo cost them nothing compared to two failed flagship flicks like Superman Returns and Green Lantern.