Actually, we do this intentionally. Because changing your setup is always a risk with live performance software, we try to make the user as conscious of the update process as possible.
By installing each new version as a complete new application (albeit one that takes its settings from the old one), it has to be a conscious decision for the user to start using the new version. Should unforeseen problems arise, it's then very easy to revert to the previously working version.
Of course, if the majority of you would prefer we make this decision for you, we can look into updating the update process.
Having said that, I agree that at least the plugin system can be improved when updating and using custom plugins. One way to do this, would be to use a separate folder in Documents to keep your 3rd party plugs. The preference to also load this folder would then be copied to the new version as well (unlike it is now).