The method of adding perks manually is too time consuming, we need a way to just add to perk point pool so we can alter skill levels and then allocate the perks.
As far as I know, there's no direct way of adding perk point through console. You either add them manually or increase lvl/xp and add perks then set level back to 1. However, the advlevel command in skyrim doesn't work properly. It adds level but no stat/perk point and I haven't figure out how to add xp yet.