Notch removed the Aether from the so-called "Beta 1.9pre4" release, when he added The End. This of course created an issue with our current Aether.
You see, there are two things required for our worlds to be loaded. It requires both a chunk generator, and an environment. Since the Aether got removed, the Aether environment no longer existed.
There are three kinds of environments currently:
NORMAL
THE_END
NETHER
Each environment is actually tied to its own chunk generator. Although we can pass in our own chunk generators which will get used in place of the environment's chunk generator, we can rely on the environment itself, and pass in no chunk generator (the value is null, or no generator).
This also means that even though we pass in a valid aether chunk generator, if we were to use an environment like THE_END, it would use The End's chunk generator in place of ours! I believe it is only NORMAL where we can use our own. I have yet to research more, but that's what it seems like. Pass in no generator, and get a regularly generated world.
When the Aether got replaced by The End, we could no longer use the Aether environment. Instead, I had to go and use the NORMAL environment, which meant that the Aether had its own day/night cycle, which was properly taken care of in our code, as well as making sure that mobs could only spawn under certain circumstances. However, that was not my intention, and I had previously tried to bring it back its own environment, only I did not know as much as I do now, and I can edit Bukkit/CraftBukkit's code with a fair degree of reliability.
Anyways, enough about how the Aether works.
Since last night, I've been researching how vanilla minecraft loads worlds, and investigating what code was removed when the Aether was replaced. I've since created a local version of Minecraft 1.0.0, which was the last version before the Aether got trashed. I have been working to re-create the Aether environment, and it's going well so far.
I expect to have the Aether's original environment (as well as Notch's original Aether chunk generator) ready to go for the next update!