If you want to get rid of the plastic containers but still keep the bare bottom for most of the tank, why not look for some glass containers to put your plants in? You can find square and rectangular ones commonly used for floral arrangements in most arts & crafts stores.
Here are some examples:
However, neither the plastic or glass containers allow water to enter the substrate from anywhere other than the top. I don't know enough about aquarium plants to say if this is a bad thing or not. Maybe ask around. http://www.save-on-crafts.com/squarevase4.html