Hi, I'd like to suggest few changes in arduino software: In os x application support files/folders should be installed in...Application Support (either of the user ~/Library/Application Support or for everyone /Libray/Application Support), the preference file should be in Preferences folder and not directly in the Library and finally the version number shouldn't be in the app name...it's already in the About screen.
The IDE is open source, you are allowed to make any changes you want. I don't think that's easy to make the IDE run perfectly on all the OSes.
As far as the version number in the name goes, you obviously haven't looked at the latest version.
Arduino libraries are code libraries, not libraries in the sense of the support stuff in ~/Library or /Library. The new library structure makes very good sense to me.
In fact, I develop on a few different machines, and your suggestion of scattering stuff into various Library directories would make it a distinct pain to keep them synced.
I personally prefer the cross platform support (users have the options of linux, mac, and windoze if you must) to fine tuning os-specific details on one platform.