For me what stands out about Mercy is its length, buildup, and general atmosphere. Now, I try to avoid the word "atmosphere" because how the fuck do you describe atmosphere in a song? But Edge's little loop and the bass sort of create this dark...mood I suppose, along with the opening line of : "I was drinking some wine and it turned to blood." What a way to start a song. The whole song has this vibe that hasn't really been present in any of the other 00's work, whether you like it or not. It's reminiscent of some of the darker 90's stuff, but also 80's epics. Yet, to me anyway, Mercy still sounds fresh. It's nothing really new for U2...it's more like a song that is the epitomy of U2. U2 at its most U2ish in a way that doesn't seem like it's trying to hard...it simply is.
I don't know, that's just my take on it. The song just works for me. I was listening to it once not too long ago and during the bridge I felt possibly the calmest I've ever felt in my life. It was a wonderful feeling.