First of I tought this is a thread about limiting building, which I absolutely do not support, later why, than talking about yellow potion --> hence there is another thread regarding that.
A building limit would restrict creativity and possibilities to expand in PVE, mind you there are small servers as well not only the crowded officials you read that much here.
I do however see why temple or vault spam can affect a server in a negativ way so for those issues I got two suggestions:
Temples:
Each clan can build one temple per god but remove the placement restriction.
Vaults:
Make it somehow different to structural stability and limit the building of vaults within a range of the first one per base, so you could maybe build about 2 or 4 in a base but not use it as wall or whatever.
When it comes to other issues like thrall bases, I will make a seperate suggestion later, new member seem to face some hard restrictions in this forum, I would propose to use the upcoming pets, like the camel, to bring the thralls back to your base so you basically would just have to build one wheel of pain, and store them in the cages.
Another option could be to make wheel of pains accessible for everyone but with a like instanciated inventory so you would basically not need to build multiple wheels around a farming spot and your thralls could not be stolen.
About travelling it would be nice indeed to have the option to go back from an obelisk to your maproom but why do I sense some PVP-players might completely agree with this idea 