So Superman will laser eye everyone, while not being affected by bullets, punches, or energy blasts.
And Batman will...........give him moral support and possibly a bagel sandwich??
from me as well... point certainly taken...
But sure, it can be done. You're right that a villain that can be stopped with a brute force takedown alone isn't going to work, because Batman will look useless. So the writers have to be more thoughtful than that. Batman has to come off as a master strategist, whether against Superman or against some villain. Again, the Red Son and Injustice storylines show possible templates.
Superman has problems with Lex Luthor, not exactly a physical powerhouse. I think Batman has at least brainpower, money, firepower and other resources that Luthor has. I think the movie will be awesome.