You can't please everybody all the time...
It could be worse.
It could be more like some of Adobe's licensing, where you actually have to remember to connect online and give the license back before you format your hdd, or it won't be available to retrieve it once you've reinstalled without calling them up.
Or it could be like Microsoft, where even though you bought it at the store, you still need to activate online. And in Vista's case, if you upgrade your system too many times, you DO have to go buy a whole new copy.
And in all of these cases, you have to buy multiple copies/licenses in order to install it on multiple PCs in your own house. MC doesn't have this restriction. Giving that, having to connect to the internet once when I install it on a new PC really doesn't seem so bad.
Personally, I don't really give MC's licensing scheme a second thought. Even if you're installing it on a PC that's not connected to the internet, you still needed to download the installer itself, so you definitely have an internet connection available somewhere to get your license.