Either I am missing something, or you really need to change how upgrades are handled. I am a paid user. My iArchitect tells me when an upgrade is available. I generally avoid doing upgrades because of how they are handled.

I got to the web site and get the new version. No "upgrade" is listed, so I download and install the free download. The setup.exe then fails, telling me I have to uninstall iArchitect first.

Upgrading should be a much more simple process - the installer should recognize that I already have the product installed and it should simply upgrade what I have - not make me uninstall and reinstall the product and have to redo all the configuration information

If you read down the list of request/suggestions, this has been suggested.
Unfortunately, upgrading software is not a simple task.
We are looking into it and will make this happen soon.