Instead of upgrading houses, I recommend having a structure upgrade system in place with stone/ore that you mine.
With the new resources each building can be upgraded. These upgrade structure provide a set benefit
Mudbrick house - 1 pop
Stone house - 2 pop
Mudbrick Bakery - 1 food per whatev.
Stone Bakery - 2 food per whatev.
You can also incorporate the advance structures into mining. By this I mean you need stone to build a temple, it cannot be done with Mudbrick.
To get Nobles, you must build a city centre of stone, which will attract migrants and allow you to upgrade your villagers.
Side note: what if there was a traveling merchant camp? A merchant would occasional come to a settlement with a trade yard (or depot) and trade resources with you?