@Wulf
Cheers for the feedback and the (awesome) screenshots. I am focusing on the RetRaider CC (standalone ret raiding version of Doctrine) at present, but I will be merging RetRaider into the Doctrine base soon. Along with this merger will come numerous fixes to the base code which should effect prot as well. This merger should happen soon.
A few points.
Regarding the Zul'Aman issue: I think this is because the CC registers the boss changing target (to use Lynx Rush) as losing agro -- therefore it taunts straight away, even though you still have agro. I thought I added a check to ensure that agro was indeed lost before it taunts, but it appears I did not. I'll have a look into this soon.
Regarding your suggestions: Hand of Salvation will definitely be implemented, as will trinket use. I completely overlooked racials so apologies for that, they will be added.
As for Hand of Protection, though, I'm not too keen on adding this, because I feel HoP is a very powerful ability that is very hard to get right in a CustomClass. There are situations where an ally is at 15% where you might want to use BoP, and others with the same health where you might not want to. This is the same for Hammer of Justice, as often in end-game raids mobs are immune to stuns, so you might be wasting a global cooldown and a cooldown. I'll look into it and see what I can do, but I can't promise anything for those two abilities.
Option-wise, once the GUI is added I will be recoding the CC to be entirely configurable. This means that you can choose whether or not to buff, automatic aura switching, movement, targeting, facing, etc. In short: definitely will be added at some point.