> Use Ekiga or an ordinary phone call.
Let's go over your list for an ordinary phone call. Here the 'client app' is your phone terminal, and the 'server' is the phone operator.
> - Is any communication not properly encrypted
Yes, it's not encrypted at all.
> - Is your communication being spied on / being recorded
I would say yes, at a similar level of probability as a skype call.
> - Is there a way to add feature "x" to the application
> - Is there a way to remove feature "x" from the application
The specs for the phone terminal are not open-source, so you can only do that with some hacking. The same is true for skype, even though there it might be more complicated technically.
> - Is there a way to use the application on your specific hard / software
Irrelevant for a physical phone.
The main difference between the skype client and a phone, is that a phone follows an open protocol, and therefore you can build your own. This is the only reason I can think of why using a phone is 'free' while using skype is not. But I think that if the skype protocol was made open, Stallman would still argue that it is not free and therefore should not be used, and therefore I do not understand his argument.