The Third Age was roughly 1000 years of growth followed by 2000 years of war and decline. In some of Tolkien's writings, you can clearly find the idea of immortals fighting the long war that slowly wore the Numenoreans down over the millennia.

Nonetheless, the immortals (including Ilúvatar, but mostly their underlings) messing with the world was a lot more prevalent in the first and second age. The third age was kind of a transition to the age of men, which finally came by in the fourth. So for humans progress was definitely positive overall if you don't just look at the cataclysms.