As I understand it, 3.6.10 will be based on the 3.6.9 branch and so will not have most of the scripting stuff in it. However, I've been pretty good about committing all my changes to CVS, so the next HEAD build should have most of the stuff that I've mentioned that I've done.
Which to use is entirely up to you. As far as I'm concerned, the period where the "new" scripting system is not in official use has the benefit of giving me a bit more leeway in case I want to change some infrequently-used parts of the system to work more closely with convention or just plain better. This is the first time I've basically written a programming language*, so I'm constantly finding new things that I want to tweak or change.
*(Technically, I only defined all the functions, object types, libraries, and implemented the appropriate code for parsing the Lua sequences and integrating that with the aforementioned elements. It still feels like starting from a clean slate, though.)