Patches we'll get simple balance changes, maybe some UI improvements, and some AI updates. Expansions can alter things, and that's probably best in the suggestion forum

As to your above:
1. Yes, it definitely needs some balancing. Mostly, we need better military policies, and worse economic ones. I also think that the wildcard ones need some updates too - especially mid-late game, when my choice is an economic policy that will make me 30-40 gold or more per turn, or a policy to give me +2 scientist points, when I'm already making 15-20 per turn? I think those wildcard ones should be more powerful, maybe the early game ones should be "each district provides 1 extra GPP of their type", with the late game being "double GPP for district+buildings". That might get me to sway away from my defaults.
2. Would love a simple change to just put religious units on their own layer, like traders, so that they are not affected at all by combat units. Just doing that alone would significantly help the religious game not interfering with the rest of the game.
3. They definitely need to tone down the warmonger penalties. Or even if they just had them as a more variable (ie. declaring a holy war won't be as big of a deal with your friends who share your religion), that would make things better. And they definitely need some way for you to ask/bribe your allies to go to war without someone who you're at war with.
4. Agreed. Needs work.
5. I do think there should be some to get more base production later in the game. Sure, if I place a city in 2000 BC it should take 30 turns to build a monument or granary. But should it still take 20 turns if I place it in 1500 AD? Even something as simple as having the base city tile yield increase by 1 food and 1 cog per era, then at least any city built in the industrial era would automatically have something like 6 production, and they can get off the ground a lot faster. It's just depressing when you place a new city and see that it's going to take 250 turns to build an industrial zone.
6. I think this could be handled by better AI. If it's wasn't so easy to conquer a neighbour early, maybe the peaceful/REX way would be better. Or if there were other early benefits to a religion, right now it just feels like if you race for a religion early, you're just going to be foo far behind the AI by the time you get it that it's not worth it.