I would prefer the two team up, maybe have some mini fights but then a larger threat becomes more important. Maybe it is time to bring in Darkseid, I just recently rewatched Superman/Batman: Apocalypse and really enjoyed the stand off between Darkseid & Batman.
Spoiler is for those who have not seen Apocalypse yet.
Also, rumors have been floating around that they might go with a Batman Beyond style era Batman for the newer movies. Basically finding someone older to play Wayne (to skip over needing Bale) and to help bridge a gap.