Ok, the indentation issues in WordPress 2.8 were caused by another plugin, SyntaxHighlighter Evolved. I upgraded to SyntaxHighlighter Evolved from Syntaxhighlighter Plus as Evolved claimed to have support for WordPress 2.8 whereas Plus is apparently not being updated anymore.
The next question I have is, now that WordPress has syntax highlighting in the backend with the code editor, can we use this function in our posts to have the native code highlighter work rather then needing a plugin?
And the verdict…. Nothing special.
The upgrade process was extremely simple. Just went through and updated all my plug-ins and theme to be 2.8 compatible and followed the three step upgrade process, and voila.
The admin interface has received a small polishing, with a new theme browser and theme installation method. I like the new editor for use with theme php & css files. The syntax highlighting and automatic documentation feature seems to be the best improvements for me.
So to sum up the installation went very smoothly, but unless you are into customising your themes or changing theme’s often then I don’t see any compelling reason to race out and upgrade.