I rather liked the arrangement of wood and stones before, it was a sort of happy jumble. The current layout is very symmetrical and rather stark. The flat stones are also covering up a lot of potential planting area (an utter horror to someone like me with severe collectoritis - must use every available millimeter to get more plants in tank!
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I can't tell if the rhizome for the java fern is above the gravel or not. If it's below the gravel it will rot, so pull it up so just the roots are covered or tie it to some driftwood or a rock. While it will take a while, java ferns can get very large (leaves over a foot long and 1.5" wide) so it helps to be able to move it easily by attaching it to a small piece of wood or rock.
You've got some great background plants with a nice mix of color and texture but you could use some fore and mid ground plants like smaller crypts, Anubias nana 'petite', and maybe a ground cover like Marsilea minuta.