It just occurred to me that the whole advanced weapon issue could be improved by making a third type of rune that carries weapon traits. If you want a better longsword, just slot the appropriate rune, and you have the weapon of your dreams. Ancestries could come with a favored rune/weapon combination rather than a specific mundane weapon.
It loses a little flavor but adds a lot of flexibility at a very slight risk of slightly looser balance. If it's an issue you could always keep certain trait combinations apart, or make certain trait runes come online at higher levels.