Religion isn't meaningless diplomatically in Civ5, it's just that you're not automatically hated for following a different religion. If another civ follows a different religion and you spread your to them, they won't be happy. But if they don't have any religion, you'll get a positive modifier for spreading, because they'll get to share in the Follower Beliefs.
I've never seen any of these modifiers come up, not even when it was spread to their capital. Did you actually see these modifiers, or are they hidden? I've seen modifiers for becoming friendly with CS's, building wonders and all sorts of things, but I've yet to see them for religious spread.
About border expansion; I'm not following how a more organic type of border expansion would affect decision making.
It's probably good to say that the speed of tile acquisition still depends on culture, and with good culture the tiles can come in fast, like a tile every 4 or 5 turns or so. The potential workable radius of your town is 3 tiles away from your centre, so normally you won't have every good tile in straight away. When placing towns this already leads to decisions to be made, like do I place my town closer to that specific resource, losing some other benefits, or do I gamble on being able to bring it in with culture quick enough? Buying tiles isn't always attractive, they get more expensive when they're further away as well.
Some other ways to bring tiles in is buy culture bombing an area or to place a citadel. That means sacrificing a great person to bring in a bunch of tiles at once. They can even be tiles that belong to other civs or CS's (just buying from others isn't possible). There will be diplomatic consequences to stealing tiles.
I don't believe they're much criticism for this new border expansion system, altough players will never stop complaining about which tiles will get auto-selected (like when a plains tile with nothing on it gets selected over a deer-forest tile, when both tiles are just as near to the capital). Although tiles that can get selected are earmarked before the actual acquisition happens, visible to the player.
You would need to play with this border expansion system first, Willem. I can understand most of your reservations about Civ 5, but regarding this aspect your criticism is probably premature.