1. Don't downgrade Superman's power level in order to allow Batman to compete. I assume there will be some sort of fight scene involving the 2, it should be made painfully clear that Superman is holding back or has been weakened somehow giving Batman the chance to compete on a physical level of any fist fight regardless of what sort of armour he is wearing.
We all saw how raw Superman's power is and what sort of impact his blows had on other super powered characters in MOS, so simply wearing an armoured Iron Man style suit, shouldn't be enough to allow Batman to compete.
2. Don't make Superman dumber to make Batman appear smarter. We all know Batman is a very smart character, smarter than Superman. But Superman isn't stupid & shouldn't be made to look so in order to give Batman as much as a mental advantage as Superman has physical.
3. Don't take Nolan's Batman route. His trilogy was fantastic in it's own universe. However his Batman & style of Batman should have no place in a world that has flying aliens & the like. So while they did, to an extent, try to keep things as grounded as they could be with a character like Superman in MOS, they can afford to be a little more brave with this Batman.
Make him smarter than he has been in any previous on screen Batman, allow his gadgets & inventions to be a little more.. adventurous. I'd happily take a Batman similar to that of what we see in the Arkham series.
4. Don't mess up Lex, we've yet to see a really great live action Lex Luthor. He should be smart & manipulative. I fully expect him to in some way trying to manipulate the public & using the fact that Superman broke Zod's neck as some sort of proof that he's as danger to the world.
That's all I can think of for now.