RE: bundled extensions - isn't the issue not that Akismet and TwentyTen are bundled with the default download, but rather that they are bundled as part of the core.svn.wordpress.org repository?

WordPress could come bundled with any number of arbitrary Plugins and/or Themes, and none of them would be over-written upon WordPress core update if none of those Plugins/Themes is part of the core repository.

Whether bundled with the default download or not, Akismet, Hello Dolly, and TwentyTen (or any future iterations of the default Theme) need to be moved out of core.svn and moved into plugins.svn and/or themes.svn - voila: no more problems with the Akismet update dance, or overwriting modified TwentyTen (though I have little - nay, no - compassion for anyone who modifies TwentyTen directly, instead of using a Child Theme).