I have upgraded WebLogic many times, but I have never upgraded a domain.
If you upgrade WebLogic within a major release e.g. 10.3.5 => 10.3.6 or 12.1.1 => 12.1.2 there is no reason for using the upgrade/reconfiguration wizards.
If you upgrade between major releases you should use the wizards. I have never done this as I have opted for just installing the new release and then redeploying everything.
I like that you get a clean cut and move as little as possible to the new installation.
The Reconfiguration Wizard only supports WebLogic 10.3.0 and never. For older releases you need to use the Upgrade Wizard to upgrade to WebLogic 10.3.6 before using the Reconfiguration Wizard.