VUO is still being developed and is cross-platform node style editing. Once it's released you can use it for free, but you won't have access to the latest features for 6-10 months after a release.
I think that giving the user the ability to change the flash parameters (just add more to the parameters field in Arena) will fix this Stage3D issue.
I could be wrong (not knowing exactly how Arena handles the interop between flash/video). I'm thinking that when an SWF is loaded, they ONLY look to see if compression is turned off so it can read width/height and frame rate and that's it, everything else is loaded as "default" which causes Flash to render on CPU.
I can get the simplest interactive 3D box to run on an android phone/iphone/ipad, emulator, browser but not in Arena.