I just realized that the chat log files are named not with the name of the one I chat with, but the one who starts the chat!
This makes chat log files messy.
For example, if I start the chat, the file is named with my name, no matter with whom I chat. So if I chat with two people, the log file mixes the chat history of two people.
And it creates files like 'my name.html', 'my name (2).html' etc, which make things even more chaotic.

Another problem is on Skype itself. It doesn't allow to reallocate its chat history to some other location, but must be in %appdata%\Skype. If I restore my system drive, the history is lost.

You've posted this in the wrong section.
This section is for Windows Live Messenger (MSN) Plus!, not Skype.

Also, I believe that the chat logging is incorrect regardless. This isn't due to Plus!, but due to the shortcomings of Skype itself.

Yes you are right. I reposted in the plus for skype bug section.
I also strongly agree with you WLM shouldn't disappear, however I believe MS is not going to revert back on this. We can only hope it will make Skype better.

Sadly that is true.
Even more sad is that both Skype and Messenger Plus! for Skype are both not even close as what they were as and for WLM. Even Plus! offers far too little functionality and even non-interface changing functionality is left out. And for some reason, I doubt it will both be changing.