I don't think anything specific needs fixing, but I do agree it would be nice to get the IDE rewritten to get rid of all of the processing-specific stuff (like the "tools" folder with Mangler inside...) and separate the code that does stuff (compile, add prototypes, upload, etc) from the GUI. However, it is a lot of work. Perhaps OP could get a few dedicated people together and ask the arduino team if they would accept a complete rewrite of the IDE as a contribution.