I started my first tank with the planting substrate (flourite) under the sand. The sand is sifting through the planting medium now and the planting medium is coming more up to the surface.
I just started another tank with ALL sand, as I don't like the look of the substrates mixing.
Planting directly into the substrate is easy to do - easier, in fact with some plants than gravel... Dwarf hairgrass is tricky with gravel, but with sand, I just dug a trench, placed the hairgrass in place, and gently dropped some sand over the top to get sand into the middle of the hairgrass... It now looks like its been there forever, but its only been a few weeks (2, I think).
The nutrients aren't a concern, as many plants (if not all) draw the nutrients from the water column, which is why most fertilizers are available in liquid form. You could add root tabs, if you choose.
I'd stick to a fairly thin layer of sand... I only went 2 inches deep on my new tank, so the compacting issue is less of a concern. I also have fish (cories) that will move around the substrate... and I've had no issue with the roots not being able to push through the sand. My amazon swords had nice long roots in the all sand side of my first tank, when I pulled them to replant in my newest tank. Using large grain sand makes sense... and will be easier to wash as well. Personally, I used play sand, which is a mix of sizes, I believe.