OP here. My ideas:
1. Thanatos destroyed the Moon, not Pluto. Who cares if Pluto is destroyed? Would anyone even notice? Or care? Most of humanity is wiped out and thousands of dragon eggs fall to earth, jettisoned off Thanatos in the collision.
2. Kazuki no longer exists (worthless character). Gio goes away in a puff of logic (I don't hate him, I just see no need for him). Raina Cromwell provides the main "rival" character for Jin.
3. Widow sort of combines that woman from the moon who Toa ran into with Gio. She's a dragon who has loved and lost and doesn't want to see Jin & Toa go the same way. Toa encounters her first, then Jin. She aids Jin reunite with Toa and becomes their ally.
4. The ISDA/Gillard Army rivalry is the main conflict. I haven't quite figured out exactly how to work Thanatos in, aside from both sides wanting control of it and the dragons that come from it.
5. Toa remains strong. I liked the strong Toa of the first few episodes, before she emoed out.
6. Less stupid nonsensical shit. Some of the stuff I read in the Dragonaut Wiki (I gave up at 15) made my head hurt.