Deadpool intentionally defys all logic whenever he needs to.
I hate to say it but you just can't win against that unless you have some ability equally illogical.
For that reason alone I'd say that Marvel would also defeat DC simply because Deadpool is a marvel character.
Now without deadpool the odds are somewhat evenly matched.
DC certainly has it's share of overpowered characters but it also loves giving them relatively crippling weaknesses (kryptonite ahem).
You'd also need to think about whether either set of characters had the chance to prepare. Batman is a great hero but much of his success comes from an intimate knowledge of who he fights. Iron Man would suffer similarly because he can't make a new suit for a threat he doesn't anticipate.
Alas I don't think there will ever be a clear answer to that question if you remove deadpool.
With deadpool marvel wins out of the sheer logic-breaking nature of his powers.