I vehemently agreed too that a MoS trilogy should be done first when adding Batman was announced, but I've thought it through and I actually think it might work. First, it has to be pointed out that, if WB didn't put Batman into this next movie, their whole Justice League set up might've fallen apart. Granted, that's not necessarily true, and Justice League might still fall apart, but the chance of it not failing have increased dramatically.
Man of Steel made a ton of money. The thing is, it lost business really quickly. Add that in with the fact that sequels rarely do as well as their predecessor, and the MoS sequel was destined to be a disappointment - not a good next step for the franchise. Adding in Batman, however, practically guarantees that this sequel will do more than the first.
Now, they can easily mess this up, but as long as this is still a Superman movie, that happens to have Batman as a supporting character in it, this can still be a true sequel. If this doesn't make the same mistakes as Iron Man 2, it can still succeed as a film in and of itself. What I mean is that if they forsake doing any JL build up and keep this from being an advert for that film, adding in Batman could work.
The other good thing is that Ben Affleck is very likely to direct either JL or a stand alone Batman movie (my guess would be the latter). Which means that he will want a say in how the MoS sequel portrays and interprets Batman. Which could mean that he might work on the script in some way. Which would mean that the main problem with the first film (inconsistent script) could be fixed on this second film.
Fingers crossed.