Here are some config options that I personally think would be very useful to have.

1. Option to enable/disable the ability of the habitat to change the type of a hatching dragon egg. (With this disabled, each egg will only spawn its' corresponding dragon)
2. Configurable Max health values for each type of dragon so that they can be tweaked within the config
3. Configurable Flight speed for each type of dragon so that they can be tweaked within the config
4. Configurable spawn rate values for each type of egg.
5. Configurable list of dimensions that each dragon takes damage in while inside.
6. Configurable list of dimensions that each dragon egg can be hatched within.

NOTES:
5 is quite niche, but personally I'd like to use it to cause the water and forest dragons to take damage while in the nether as if they're on fire. I'm sure others may come up with their own use cases for it though.
6 is niche as well, but I'd like to use it to help put the feeling of exploring a large world back into the other dimensions (nether, and the end) that gets taken away once you've gotten a dragon.
Overall, these would be great for people like me who love the mod, but are finding some eggs are quite common and can then be turned into any other egg and make exploration extremely easy for other dimensions when it shouldn't be. For example, after getting just one dragon/egg, elytra become obsolete and you can fly to an end city to find them. With the configs suggested, one could easily make it so that only end dragon eggs can be hatched inside of the end, and that all other dragons take damage inside of the end dimension, effectively forcing players to search for end cities and their loot on foot.
Alongside this, suggestion 1 introduces rarity to the different dragon types which could be great for trading on MP servers.

I would also like to be able to configure this mod... Or at least disable spawning in dungeons. Getting to the end is much harder than just stumbling on a dungeon.