Here's the thing... those are are marketing numbers, not version numbers. If you go by their internal version numbers, they make a lot more sense, and better reflect incremental changes vs total rewrites.
Windows 2000 - 5.0
Windows XP - 5.1
Windows XP 64-Bit/Server 2003 (incl R2) - 5.2
Windows Vista/Server 2008 - 6.0
Windows Server 2008 R2 - 6.1
Windows 7 - 6.1
Windows 8 - 6.2
Windows Server 2012 R2 - 6.3
Windows 8.1 - 6.3
Before Windows 2000/XP, there were two completely separate OSes (NT and DOS), rather than simply different editions of the same OS. Because 2000 and later are the successors to NT, that's why it starts with 5.0.
So why did NT start at 3.x? Because it started life as the successor to OS/2 1.3 and 2.0, known as OS/2 3.0. When it shifted to become Windows rather than OS/2, it kept the version number.
The DOS based Windows go: 1.01, 1.03, 1.04, 2.0, 2.10, 2.11, 3.00, 3.10, 3.11, 3.2, 4.0 (Win95), 4.10 (Win98), 4.90 (WinMe)
Windows versioning numbers makes a lot more sense once you separate the marketing name from the actual version number. MS Office works the same way (e.g. Office 10 is Office XP).