The reason it is being in 4.99.1 for too long time is just we wanted to include all documentation and then real life took over and we've been discussing release for the last couple months already, there are still some things to be complete but overall it is very stable. I use it daily in multiple installations and it is being used in many production sites around the world. Ask Zoran, he uses it for their product for a long time already. Tcl API does not change, the one of the major goals is to keep backward compatibility, may be not with everything but at least on Tcl level.
As for going in different direction than AS, that is true, we ported some stuff from AS 4.5 like new adp parser, pools, Tcl initialization but adjusting to our vision. Overall i think it is much better server than AS 4./4.5, it has support for many many features, a lot of modules and integrated many commands so no need for extra modules like nscache, nsha1, upload statistics for huge uploads, writers support for delivering huge files without using conn threads, embedded virtual hosting, no need for config or server restart to add new virtual hosts.
Also, docs are mostly up-to-date, for quick overview see:
http://www.crystalballinc.com/vlad/software/naviserver//index.oss?&tab=docs
Sorry for advertising, i did not post here for a long time.