I liked it better when the common consensus on the fate of the Dragons was that they were eaten by the Tsaesci.
There's a dev RP going on that involves dragons, and there's a post that says that most Dragons peacefully assimilated into Akaviri culture, and the remaining Dragons fled to Skyrim, led by Alduin.
Regarding the humans being able to defeat the dragons, well I wouldn't say only some of them could use the Thu'um. I reckon at the time that every Nord could use at least some form of the Thu'um, although much weaker than a Dragon's Voice. But there were a lot more Men than Dragons. Think bees overpowering wasps, or even birds.
And then the development of Dragonrend, and it was pretty much gg for the Dragons, with the exception of Alduin. The Thu'um of the ancient Nords was fueled by pure hatred, whereas the Dragons could do no such thing.