Some of the data .Mac syncs does not track the date/time of update in its native file (e.g. bookmarks), so you need a respository to track the dates of all the updates. .Mac provides that, and also provides a way to synch so all of the synched computers don't need to be turned on and connected.
How do you suggest doing it between two computers without a server holding the data (and tracking the updates) somewhere?
It can be done, but it's much more difficult, and the user has to understand the implications of where to store the sync data, and when/where it is available. This is not the type of user Apple is targetting with .Mac sync.
If you want that capability, you should look at writing your own utility, or asking a developer to write one - it won't be easy.