I don't think the Paludarium idea would work in this situation. I don't want to have any other animals living in there (bf would freak, I already have a zoo of furry creatures) and if the upper level fully covered the lower, I'd have no ability to change the water in the fish tank part. Neat idea, though.
I'm just not sure I want to use a piece of glass in the centre, but I think the concept of putting a barrier in the centre is a good one. I'm not sure yet how I'm going to pull it off, but I'd like to have a hole in my barrier through which I can run a pump hose (off the filter if I can), and have it basically pour water out on the plant-side to run down a little stream and then back into the fish tank. I think I might end up having the barrier go about 2/3 the height of the tank (haven't measured it yet) but I'm not sure if I'd put the plants up that high.
What would I need for a top on this whole thing? I have a wire-mesh cover now. Would I need to get something a little more solid (or alter the one I have to be solid)?