The Nature Shrine should add up every year, until the limit is reached (250% for planets, unless the shrine allows them to get all the way to 300%). That is, if you are playing with unlimited resources. On the other hand, the Condition increase is a multiplier, so 3% is very weak for planets with poor conditions. The values for the conditions range from 0.1 (Deadly) to 1.5 (Optimal), and so low values take a lot of time before you can recover from them.
You may also want to decrease the costs of the VI II and III facilities to avoid the "sneaky" way of building the first level facility and upgrading for a lower cost, as some players may go with this kind of trick (or loophole, as you will).
I am certainly not against weakening the Nature Shrine, or stretching its levels beyond level III (I will take Religious in the PBW game, so it isn't a fit of Religious-phobia). I must also admit I am intrigued by what you plan to add to the Religious trait.
