I have not seen it discussed, but I think that armor checks should still be double penalty while swimming. There is really no way to swim while in armor in real life. I like the new skill and feat combinations after using them. I love the PF RPG and how skills are handled. But since you will give ear to the customers.....please, dont allow armor checks through at single penalty. If 3.5 did get something right...it was that.
Thanks Paizo!