I tested penetration recently on a target skeleton. 331 penetration gave 1% extra damage, which surprised me. I had thought 500 pen was needed in PvE for 1% damage. I tested with a stam DK, but assume spell pen should be the same.
Once I looked at my CP and how they scale, this meant that a roughly even distribution between Spell Erosion, Master-at-arms / Thaumaturge, and Elemental Expert yields the most damage.
In general you might prefer Spell Erosion over Master-at-arms / Thaumaturge and crit to buff your procs, such as Zaan / Skoria. IMO not worth it in PvE, but can be worth it on a PvP proc build. On the other hand only bosses have the full 18.2K resistances. You might go easy on Spell Erosion if your group is well coordinated and because it does nothing against some trash mobs.