Armored cruisers were useful despite later obsolescence

Would most navies have been better off building protected cruisers instead of armored cruisers?

No. Armored cruisers were genuinely useful for the missions and strategic conditions of their own period.

A blanket substitution of protected cruisers for armored cruisers would be mistaken. The larger ships combined endurance, protection, and combat power in ways many navies valued before battlecruisers and dreadnoughts changed the threat environment. Their later vulnerability does not erase the roles for which they were originally procured.