The old upgrade system did like a flat increase in item power, so your 925 weapon with a 5/5 upgrade was in effect a 950 weapon. Now we have masterworking which dosen't change the items base damage or defence but instead increases the magic affexes each time you masterwork. In most cases (aside from maybe a few unique weapons) a 12/12 masterworked item will be better than a 5/5 upgraded despite having lower base dps.