Everybody will start with all skill levels set to 0, because the new database table won't have any data to start with.
However, this is only a matter of a couple of hours before your characters maxes out. Remember the skill levels system has been originally designed around the Campaign mode, which is 3 maps only! It is obviously not easy to get all levels in only 3 maps, but it is indeed possible. Most people will reach max levels in a few evenings at most.
Also, if you guys want to try it out, the official test server has been running the prestige feature for a couple of weeks. We're polishing minor details before delivering a new snapshot to TM. Disadvantage is that you'll play mostly against boring bots there.