Given that Batman is in the sequel, I'd like to see Bruce Wayne show up in Metropolis and have Lois and Clark meet him. He could be helping with the redevelopment. There could be rumors of Batman being seen in Metropolis at night, and Superman could run into him. Maybe they don't hit it off at first, but by the end Superman could decide that Batman is more or less a good guy. If they keep Lois and Clark the point-of-view characters and minimize Batman's screen time, I think it could work, even while doing all the other things that the sequel needs to do, like establish Clark at the Daily Planet and establish Superman's relationship with the public.
Do I think they'll pull it off effectively? Nope. But I can hope....
My favorite Superman Meets Batman story is World's Finest - the three-episode crossover between Superman the Animated Series and Batman the Animated Series. I don't want them to just use that plot, but I hope they draw some inspiration from that for their relationship.
Incidentally, World's Finest has Batman throw Superman across a room and then expose him to Kryptonite the first time they meet. It wasn't a prolonged fight, but it could count as Batman beating Superman. So if the quote from the article means that they're going to have a fight in the movie, I hope it's more of a short altercation when they meet like World's Finest did. (Though I'm not sure movie makers are physically capable of having Superman and Batman fight each other without overdoing it.)
All in all, I would prefer to have the sequel, then bring in Batman for the third movie. We could have a separate Batman movie before they combine, but I don't think it's needed given that we just had a Batman trilogy showing his origins. I don't think that Batman being in the sequel is necessarily a disaster, though.
