I organize my dragons based on one criteria: Element of highest earning habitat at Lv. 2.
-Pure & Primal: 240000
Examples: High Celestial is in a Legend Habitat. Crested Fae is in a Light Habitat. Flaming Rock is in a Flame Habitat.
Exceptions to this organization:
Ancient World Dragons are organized into 5 habitats, 3 per habitat. There is no Magic Habitat on my islands.
Pure and Primal Habitats have the same amount of Max Gold at Lv. 2, so it's just preference here.
My plan is just to upgrade one Habitat to max before moving on to the next.
Exceptions being Terra and Flame.
Terra: One Terra habitat should be enough for Terra and Double Terra. A Lv. 1 Terra Habitat should be fine. I have a Lv. 4 Terra Habitat only for simple Terra+Terra and Terra+Flame breeds for Chests and Races.
Flame: Only 10 Dragons that need a Flame Habitat right now. Two Lv. 3 Flame Habitats should be enough for them.
Have not looked much into Sea or Nature, but they should also have few Dragons to them as well. In fact, Pathfinder was placed in a Nature Habitat.