Quote from AnonTheMouse
Okay, I'm noticing a big inconsistency in some of the suggestions I'm getting. The End should gradually transition to something while you watch...but it should also be barren? What exactly is it transitioning to, then? I think that one key thing is that the appearance of the End overall needs to change. There has to be some sort of recognizable change from Before to After, other than just more tracts of Nothing to explore. As an alternative to fungal, however, I could see utilizing crystalline structures or coral formations, though that would usually indicate aquatic life. There should definitely be something, though. What passes for life in the Nether is generally small and low to the ground. This makes me think there should be some tall, soaring things in the End.
I throw my support behind crystalline "biomes", for lack of better word. Crystals already grow (though, admittedly, in a different way than living things) and nothing says "life, but not as we know it" better than silicon-based organisms.
What's more, end stone looks to be rather porous, which would provide nucleation sites ideal for crystal growth (if we flub the science a little bit, which shouldn't be a problem since we're talking about an alternate dimension in a fantasy game).