I'll be honest with you... your infusion altar "room" looks a bit small. Iirc, the altar looks out in a 12 block radius on the x and z for stability. Otherwise I'm quite liking your layout
edit: (Not saying your giant under-room doesn't cover that, but I'd be careful about placing things above/around)
Eh, I know the altar checks around the area as well, but honestly I almost never use anything on the same level as it. My most version before this pack of the altar, there wasn't much that looked good above ground, and I ended up just filling the below chamber with zombie heads, because cleaver + spawner + Ender IO's vat.
This time I might make use of the extra space above ground, but likely only with the glimmering mushrooms, since those are new, look pretty, and probably won't tank my framerate as hard as the floating flowers do. XD
Side note; another reason why I didn't use above ground before, I've only filled the walls and the first lvl of floor down there with "junk" items, and I've already got around 140 stabilization points. Which should cover the possible 25 of random instability, along with most of the minor to moderate recipes natural chance.
I wanted to share the progress of my base so far. I don't have a strong essence stone yet and just opened up the witchery questline to give you some idea where I'm at. I like to play slow and enjoy building and exploring mods.
http://imgur.com/gallery/9j50L/
Lol, I love your idea with the ore plants in the mineshaft!