Actually, Ironman has been EMP proof for quite some time now. He was also trained in martial arts by Captain America. While he would still likely loose a fist fight with the Capped Crusader, he could still hold his own. Also, goodluck catching Stark defenseless, many have tried and failed.
Besides catching him off guard, we saw Tony go all Mission Impossible in Iron Man 3(?) and get into a facility without using his suit. Besides, why does he NEED to face Batman alone?? Tony's not an idiot, he has a solid team behind him to help. Let's see Batman face up to the Incredible Hulk. "Puny bat"!
batman is the best