Is it possible ...?

[Piru]

yes

[Piru]

Thread with such an informatime topic deserves as informative answer.. ;-)

[Piru]

1. Start regedit.
2. Go to "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon"
3. Edit "Shell" key, change it to whatever command you wish to start. In this case something along the lines: "C:\Program Files\WinUAE\WinUAE.exe" -options.

If you wish to make UAE start automagically with some given configuration use options: -f "C:\path\to\config.uae" -s use_gui=no

[Piru]

But with replacing the registry key, it boots straight into winuae without loading up the win desktop?

Correct.

Could be interesting having two win partitions one for winuae exclusive and another for daily usage

That's probably a good idea.

Then again, if you need full Windows desktop too, then why not just run WinUAE from a desktop shortcut when you need it? That's way faster than rebooting the system.