I am trying to do the natural tank thing. My old tank was natural and was beautiful, but its because it had many years of mulm in the flourite substrate.
In the new aquarium, I did put in the 1" soil layer, then a couple of inches of flourie. Even w/ the soil, it's still a new substrate. I have high hopes for when the plants get established. I think these are just growing pains, so I might have to dose ferts for a little while, but things should eventually start to ballance out on their own.
I have been thinking about the lighting. The tops of the plants are now about as far away as the gravel was in the old aquarium. The plants directly under the halide look far better than the other plants. That is sort of the problem w/ halides. The point source of light is great, but the edges get dim quickly.