Since the the Culture-related Piety Social Policies are presumably being moved into the new Aesthetics tree, we can expect at least some changes to Religion in the new policies that will fill out the empty spaces in Piety. And, as mentioned, International Trade Routes and Tourism are supposed to affect and be affected by the spread of Religion.
I would like to see Religion better integrated with the diplomatic system. Currently it's almost all negative: unless you're playing with an unusually large number of civilizations, nearly every major civ will develop its own religion, and even if it doesn't actively spread it, it will react negatively if you try to spread yours. It would be nice if there were sometimes situations in which another civilization will allow or even encourage the spread of your religion, or will try to seek permission to do the same (or ask you to convert voluntarily). Now that different religions have different characteristics, there's the potential for some interesting player choice there... but right now, the player doesn't really get to choose; you're pretty much stuck with whatever religion you found, and your only choice is whether or not to actively spread it and whether to actively resist the spread of other religions.
I think making this more interesting this would be best facilitated by allowing the player to manually choose a State Religion, as in Civ IV. You could choose any majority religion from any of your cities, and the status as State Religion could help the spread of that religion and hinder the spread of others (perhaps dependent on the Social Policies you've chosen). This would put player choice back in the equation, and give you something important to haggle over with other civilizations.
It would require some changes in the Religion interface, as currently each Religion is inexorably tied to a specific civilization. Allowing the player to switch State Religions will probably mean having to allow a civilization to be in control of more than one religion, which I think is a good thing. Some civilizations did found more than one religion, and if you conquer a different Holy City and want to convert to that religion, this should be an option. This would also make Holy Cities more important; taking a Holy City could give you control of that religion, but only if you make it your State Religion.
I would also like to see more available icons/names for religions to found, which would be very easy to add.