Rework pen, introduce more pen items, cap pen.
First, I don't actually like item caps like in smite 1, but I think specifically for pen it should be had just like echo tenacity etc.
What I suggest is changing pen to give 15% + 1% per level (change the maths to be the same total pen for exe and totem) but then give each pen item a unique passive ontop (add a few more pen items for both str and int) this would allow more build variety which I think would be a welcome change whilst also making pen scale throughout the game.