TYPO3 Core

But when you install TYPO3 from scratch, having an upgrade wizard popup immediately would be unlogical as well.

Another aspect you have to consider is that the minimum requirements may have changed between your old and the new version. Taking this into account I think it actually makes sense to check things like the basic configuration and the system requirements first.

I think the TYPO3 Install Tool Team would do good in simply checking some other CMS Install Tools as most of them check requirements first and alarm if something is missing. In some than you can choose if you wanna upgrade or install new. If you install new than the upgrade wizard does not start and you get a clean fresh DB or one YOU can upload
If you choose to upgrade than the upgrade wizard starts step by step and leeds you through the process.

Usability is very important in install tools IMHO! The TYPO3 Tool has a lot of options but absolute no order or logical structure and this is the main problem. Reorganising the structure in a logical way would make sense.

The WEC had a nice "system requirements checker" perhaps this could be integrated as first step.

a system requirement check is implemented already. ;)

well might be but where do the results get listed i.e. if basic configuration is not accessible! ;-)
In other CMS simply a scripts lists all necessary information even about some versions installs.

"Hi I found it - Version XYZ - OK (green hook)"
Than in some CMS you see a rotating icon as it is checking another stuff and marking it later red grey or green.