I think the problems with religion in Civ, and by the looks of it Civ7 in particular, is that religions belong to civilizations. It's a specific civ that founds religions, gives it beliefs, spreads it, and reaps benefits (both yields and legacy progress) from it. This is great for player agency because it makes them a complete theological autocrat. But I think it's bad for historical flavour, and it's bad in making religion something distinct from existing game systems (specially in the way missionaries mimic military units). An alternative would be to have religions be something that civilizations have to harness, rather than create.
One way, suggested elsewhere, is to make IPs found religions. The player then has a choice: adopt the religion of the closest holy IP? Or the religion that's already popular with neighbours? Or the one that's spreading the most to the new world? To add beliefs to a religion you'd have to be the suzerain of the holy IP. This offers even more choice: do you become close to many religious IPs in the ancient age so you're well positioned once they start founding religions in the Exploration era? Do you invest in one religion super early? Or do you wait before backing a winner? Or do you try to monopolize suzerainty of multiple holy IPs to try to lock other people out of developing a religion? Finally, to get the legacy progress that requires religion you'd have to diplomatically annex that holy IP. Religions could spread passively outwards from a city to its neighbours and along its trade routes. Rather than being built, missionaries would be replaced by an off-map "conversion charge" that would increase passively at a rate that increases with the number of buildings and relics associated with a religion; and be used to either convert cities (only if connected by a trade route or close to a city already of this religion), or to inoculate a city against foreign conversion.
Such a system is not fully fleshed out here of course, and there are obviously countless details to pin down. But it would make religion something that civs fight over to control, rather than something they give birth to. It would make it that one civ could (indirectly) control multiple religions, or that multiple civs share one religion. It would make religion central to diplomacy for the exploration age, and make it as much about the influence yield as culture. It would get replace religious unit micromanagement with meaningful high-level decisions.