Well, regarding BBCode changes: I would not add too much stuff. This boards parser is quite configurable, and defining allowed nesting is not hard but one of the results of nesting too many tags is that sooner or later, posts will break the parser. I've seen that with vBulletin. Don't ask how many posts I had to manually fix in the last two years.
Regarding AJAX stuff: I have no issues with AJAX, if used with a sense for necessity. But first things first, next on the list of fixes are:
syntax highlighting. I am re-enabling the [ code=... ] stuff soon, my tests yet have worked, only a beautiful style is missing for now.
better URLs. Readable stuff is nicer, we'll have that too very soon.
caching. Yup, might sound overrated, but helps if you do not have to ask the database to act for every request.
A bit more work is required to fix the issue of properly storing the read topics. This will probably take a few days, until I can work out a sane approach to fix that.