Not really. While you can't change the underlying site  definition,
Features can be activated and deactivated at the Farm, Web Application,
Site Collection, and Site level.

So, if the changes that you want are bundled into a Feature, you can
grow existing sites  to have whatever functionality that you would be
changing the site definition to get.

For example, a Blank Site in WSS v2 will only have the latent
functionality that it had when it was created. But in WSS v3, you could
grow a Blank Site into a Publishing Site or to have whatever
functionality you bundled into a custom Feature.