Program names and "pollution"

Also it's not hard to rename commands. Rename them in one major version, provide the old ones as symbolic links and display warnings when they're called by their old names that they're going to be unavailable in the next version.
Once that one rolls around remove the symlinks and you're done.

Will it break some scripts somewhere? Yeah. But then it's the fault of the admins running it for upgrading a major version without checking the changelog.