The Linux kernel was overhauled majorly towards the release of 2.0, and then massively for 2.2. Major portions were rewritten for 2.4, which had some big advantages. It bears no resemblance to Minix under the hood - that's a joke.
But that's not fair for a comparison to 'Windows', which is much more than a kernel. Have the codebases to KDE or GNOME have been overhauled? Yes, each has been undergoing massive development in the past 10 years, and they are more stable and sophisticated than ever.
In the Windows world, MS was so sure that even XP was not much of an advance over Win 2000, that they didn't even give it a new version number... let's count. NT 4... NT 5 (win2K), XP (?), Vista (Windows 6), windows 7. Where did the extra number go? Ah yes, XP is basically Windows 2000. They spent that 18 months fixing bugs and dreaming up a new name.