Well, i havent seen the final stats, and i certainly agree, that they should be cheaper, but in my Version (preview)
the nature shrine stats look like this:
+ Nature Shrine I
2k/6k/2k resources / 1% value and conditions
+ Value Improvement plant I (100k each) + Climate Control Facility I (8k each)
--- so 108k resources vs 6k resources for the same 1% (in build time, this is say 5 turns vs 80
+ Nature Shrine II
4k/12k/4k resources / 2% value and conditions
+ Value Improvement plant II (200k each) + Climate Control Facility II (10k each)
--- 210k vs 12k resources
Nature Shrine III
10k/30k/10k resources / 3% value and conditions
+ Value Improvement Plant III (400k each) + Climate Control Facility III (12k)
--- wow, 412k vs 30k
I think you got my point, if thats not enough, we can add, that nature shrine is system wide, so you only need one for the entire system, instead of two normal facilities every planet. Well, this also means, you can only have one affecting the system at a time, but considering the build costs of the normal facilities, its unlikely, one will ever build one, not to mention multiple ones.
Should religious facilities be cheaper? definitely, are they cheaper now? Nope - they are practically free.
Would they cost half of the price of the regular one, we could argue about it being fair or not, personally i think, that the system wide ability, and that its basically a 2-in-1 structure justifies an even higher price than the normal facilities have.
Lets not forget, that is rather easy to reach research wise (at least it was Last time i checked), and that the 1500 points the trait costs you is not paid for 'free value improvement on every of your planets', but for 'access to otherwise restricted technology'.
Sorry if my post sounded a bit like ranting, but i had a hard day behind me, and had to release the steam valves somewhere
if you feel insulted by my post / tone / whatever, please acceppt my apologies, its not meant to flame or insult anyone.
-- EDIT:
Reading trough the post a second time, it is half as worse as i expected. Lets just say, my built-in cooling system works like nothing else. It also had a terrible grammar and some weird typos, which im too lazy to locate and correct