Right now, biomes only seem to affect a few things:

1. Surface decorations
2. Ground blocks above the stone layer.

That's like ... "beauty is only skin deep".

I'd like to see something new, something like, I don't know, the ability to have ores only spawn in certain biomes?

Oh, wait -- 1.3 is adding that natively -- emeralds only spawn in extreme hills.

http://www.minecraftforum.net/topic/1013348-underground-features-as-biome-dependent/

This isn't a new idea. I can see such things as:

1. A special ore that is normally only found high up in extreme hills -- http://www.minecraftforum.net/topic/1224140-game-balance-idea-for-new-ore-mana-rich-enchantability/
2. An API for people easily add things on the surface. http://www.minecraftforum.net/topic/1024204-more-structures-project/
3. A way for other map generators to make use of EBs' -- Biospheres, Mystcraft, Wedge, etc.

I'd like to see something new, something like, I don't know, the ability to have ores only spawn
in certain biomes?

Ore distribution will be taken care of by @marcopolo1613 when he gets this mod working with custom biomes.

An API for people easily add things on the surface.
http://www.minecraftforum.net/topic/1024204-more-structures-project/

A way for other map generators to make use of EBs' -- Biospheres, Mystcraft,
Wedge, etc.

This is already possible...but those developers have yet to take advantage of it...I have been working with @XCompWiz. He is designing an API that EBXL will use to provide integration with Mystcraft.

The surface API is also already available within our API...the process is no different from adding trees or flowers and can be seen in action in the RedPower plugin in this project.

We appreciate the feedback!

I am closing this issue because the specific features are already available or imminent. Please contact me privately for guidance in these topics.

(grumble grumble neither preview nor edit, and it didn't format how I expected).