I've got a lifeproof case and take my phone out on the water with me all the time. Even put the phone in my pfd pocket.
1) The phone can get really hot in the case, especially while plugged in. Like if you're playing music through a car or boat USB port. I believe, no science here, that adversly affects battery life and phone performance.
2) Not all accessories connect easily: If you use a non-apple set of headphones or charging cable, it can be difficult to connect. At least on the 4/4S case. To use my headphones, I need a special adapter cable. Not a big deal and protects the waterproofiness. To connect the charging cable, on the 4S case, you need to unsnap a door at the bottom port and connecting the cable can be difficult. Lastly, the Lifeproof armband is massive.