Windows installation has been not fine by any stretch of imagination. It still has the same problems:
1) It is third party service, not provided by system (yes, I know about Microsoft Installer); it is up to the application vendors what they will use,
2) Installers can litter in the system, wherever they want (see your complaint about Start menu),
3) No 100% working uninstallation and/or repair, you will end-up with installers damaging your system and having to reinstall (even Microsoft ones; how the heck do I get rid of CJK IMEs, that Proofing Tools for Office 2010 "helpfully" installed?),
4) No update service, you end up with many updaters slowing down your system,
5) and many more.
If you think, that Windows installation is fine - have you ever seen install systems on other OSes?