if you do have a choice between the 2, armor pen is likely going to offer better returns (increase your damage by more) unless you have 20% resistance ignored somehow already. but over all, you don't need to upgrade your gear much as you level. just take whatever drops or is given by a quest. always take weapons with higher weapon damage though regardless of what the stats are since weapon damage is the best increase in you actual damage dealt
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Stats in module 6 scale a lot more linear so you'll never really reach any cap at all. However, the previous commenters meant that enemies in PvE have only up to 60% Damage Resistance. Armor Penetration works non-multiplicative. Speaking 20% Damage Resistance on an enemy monster will be negated by 20% Resistance Ignored (this is the stat that Armor Penetration grants you). Armor Penetration will be your number 2 priority for dealing damage in PvE. First is Weapon Damage this is determined by your Mainhand. Previous to lvl 70 most of that doesnt matter as leveling is very easy and only a prolog to the actual content of the game. Critical Strike is the best late game scaling stat for damage dealers after Armor Penetration. It is very easy to aquire 60% Resistance Ignored with your gear and not even focus on stacking it. However, your focus as a new player will be to aquire lots of HP up to 80k or even 100k to stay alive in PvE content.
Use whatever gear you can get while leveling up to 68-70; as, the only problematic NPC that need some resistance ignore are the giants. If you are going to fight level 70 NPC, it's a very good idea to get armor pen of at least 40-50%. The campaign zone all require a decent amount of armor pen, This is a link with the values needed :
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For PVE, the cap of ArP is about 60%. In mod 5, I think it was 20%.
http://www.arcgames.com/en/forums#/discussion/1194234/regarding-to-the-arpen-needed-in-the-campaign-maps/p1