I wanted to thank you for a great plugin. I however have noticed something one of you other uses did. Though i have a little more elaboration on the matter.
When i create a multisite network install. The first site always is installed as http://domain.com, I have to manually go into db to allow the main site to use www. Now this causes no problem, it is just a quirk of WordPress that i have to do this. All new sites i create have different subdomains when i create them manually. It is the NS Cloner that looks at the hard value of the main blog www. and then creates a new clone as subdomain.www.domain.com
This is a quite common scenario, which in my example is implemented at least on 25 networks we operate. Your plugin, whilst useful, does not have any manual overide options or checkbox to remove the www in these instances.
Would you consider resolving this as part of the paid for plugin perhaps. If you were then i can imagine it being used a lot more in projects by my company at least, though this problem can not be unique to us in any way.