Hi Groovaholic I believe the plugins will mainly be compatible, but certainly not 100%.
From my understanding the Unity engine handles pivots different to JMonkey (which is how the UI knows how to display rectangles, lines, images, etc.). So any current plugin that uses any UI elements will certainly have a problem.
I suspect the majority of console based plugins will still work okay though.
As for LUA scipts. . . does anyone use them anymore?