Plus there was also that Guardian's Blessing buff in the early days of 1.0 that you could envoke when starting a levequest that was different depending on the guardian. But that was removed in a patch (I believe the /pray command replaced it?).

But yeah, I don't think there will be any real bearing on the game in ARR other than some minor story aspect as to your character's chosen deity - in 1.0 I just went with Azeyma for several reasons: She's the traditional guardian of the Seekers of the Sun miqo'te clan (which my character is a member of), plus Azeyma is the closest parallel to Altana from FFXI, who my FFXI character was a devoted follower of.

So I think it's just going to come down to which one you like the best.