Tom had some ideas on creating a whole new code chart from scratch for proper Arabic that is ideal for scholarly research in Level 2 plain of Unicode (so it would still be under the umbrella of Unicode). Then there would be a well defined conversion scheme between Unicode 06xx block and this new codeblock. He can perhaps give us some insight after he's back from his conference.
But that would be a long term project and I wouldn't expect anything solid within the next five years.
Surprise! Already did that. ;)
I'll give you a few brief ideas of what I tried to capture:
etc.