I'm keen to hear if anyone feels the redone preferences menu is a step backwards rather than forwards: it's back to a simple menu structure, but it provides more direct access to the parts that are important to customise.
Not mentioned in the release notes is the addition of per-project options to the API (accessible via window.project().options()), and a 'Tools/New Plugin' menu command that fills in a simple template, and sets the current directory to the Packages/User directory.
The new format for .sublime-build files (old format ones are still supported) is also much saner, here's the contents of JavaC.sublime-build:
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build javac.exe "$File"
The 'build' option is the command line to run, and the 'lineNumberRegex' option is used when double-clicking on the output window (first group is the file name, second is the line number, and third, if any, it the column number).