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1.6 moved from the previous individually adjustable stackable stats to a Major (larger) and Minor (smaller) buff system that is non stackable. This resulted in nerfs for some items and a bigger nerf for builds that relied on the stackabilty of the old system.

I could see how the old system would be a pain for them to work with, but made for a more interesting game for us players. The new system, easy for the devs, bland for the players and a lot of abilities and passives are much less useful now.

The new system makes tweaking impossible. The two level system does not give them the ability to make a change without it putting the skill or passive into a situation where it competes with or is the same as another.

I had Combat Prayer before the 1.6 respec but I went with Blessing of Restoration. I can't remember why and I can't see the stats of Combat Prayer now to compare (another flaw in their design) but I see that BoR applies the buffs Minor Resolve (increase armor) and Minor Ward (increase spell). The only way they have to buff that would be to switch to Major Resolve and Major Word but I would guess that would be too large of an increase so they would never be able to do that.

Since I can't see the new stats for Combat Prayer, I would have to assume the situation is similar.