While base size can cause lag, the biggest issue is FacePunch not optimizing the loading of items. If you have a big base its best to have just walls without windows. Why you may ask? Well FacePunch for some reason has it that when you can see the items inside a house, for example a large wooden box, all the items in that box is loaded by the server and player. Also any type of NBT data associated with that item and all other items get loaded. If you have a box full of clones, all that data, including the genes of the clone, get loaded.
I know many have called for windmills to have a cap limit. However windmills were optimized last year. The biggest lag causer currently is people building big bases and using window walls. I know it may not look the best, but try using less windowed walls.
