I like to use the nature shrines, they improve planet conditions AND planet value for the whole system. System wide facilities just stack with planet affecting facilities, e.g robotoid fac. (planet) plus Time Shrine (system). So I guess a nature shrine wouldn't even stack with a value improvement plant.
I've always had one in both my systems. It's just that now the atmosphere is converted on my religious colony, so I tried building a new one before I scrapped the old one