One big thing we've discussed a lot is the disappearance of the Dwarves. There are a few quests in the game that deal directly with this subject, but never give you a clear answer(the experiment the mage tried but carried out improperly, the Dwemer puzzle box, etc). Before we found out that Falmer were snow elves, we initially thought that the dwarves may have mutated into them. What I believe Skyrim and the other Elder Scrolls games before it have pointed to the cause of the mystery at hand, was an ascended intelligence scenario. The dwarves were so far advanced in technology, they were able to build puzzle boxes that could keep out Daedric gods. They had robots, facilities that produced power and maintained themselves. Their alloys were some of the strongest alloys(only being overshadowed by ebony as far as natural materials go). If you remember the experience the mage tried to recreate, he had a tuned soul gem that he struck with Keening to create a teleportation frequency.
My theory is that the Dwarves created all elven races in their images as infant races and then traveled to another dimension where they could see them grow much in the same way the History Channel views "Ancient Aliens" today.
Thoughts? Ideas? Your own theories?