Aight Tunaha, I'm back and hopefully you are actually paying attention to my feed back and using it in your updates (I gave you ton of feed back on monk, but you never actually replied. Nor have you contacted me T_T )
Okay so here we go with prot paladin (My new main, and previously my main for all of wrath/cata first and up to the first few months of SoO)
I'm not level 100 yet So I can only state anything that I currently have access to, and will update with new information once I'm 100 and if I experience anything there.
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Prot Paladin Spells and Issues
Scared Shield
Scared shield, Currently tracking its up time, its ass if I let it run on its own it drops as low as 40% uptime, meaning I have to begin helping it out myself. Scared shield is a spell that last for 30 seconds once applied, the spell its self have a 6 second cooldown. In order to get the abosulte best up time and use on it with a CR, Since CRs from what Im aware can't track resolve , normally I'd reapply Sacred shield my self with either high resolve or when its about to fall, is to have the CR reapply Sacred shield every 20 seconds, as of right now sacred shield is falling of and staying off for a good 2-10 seconds.
Word of glory
WoG Is essentially a "Oh shit" button for prot paladins when lower then in my opinion 50-70% hp. Right now WoG is not used at all and there is no option for it in the CR, and I have to do it manually, which is a struggle when the CR is constantly using the holy power needed.
There needs to be an option implemented for Prot paladins specifically, which gives you the option to set the amount of holy power and Bastion of glory stacks it uses WoG, as WoG should be used at 5 stacks of Bastion of glory and 3 holy power, but some times in a pinch is used at lower stacks/hp, so the amount of stacks in which the CR uses WoG needs to be capable of being picked by the player.
Bubbles... All of em
This might just be a personal issue, and I think I may have fixed it. But I was having issues where the CR was constantly bubbling people under 60% hp including myself, so I ended up turning off anything to do with hand of protection.
Holy Avenger
This is as much of a DPS cooldown as a survivablity cool down. With experience using your Monk CR I'm more then knowledgable that you are capable of setting up multiable options to have for a single spell that you can switch between / have active at the same time. Holy avenger should have an option so that it activates on a certain amount of Hp as well as on cool down / burst, with an option to turn that off. So if you didn't want it to pop just cause you were at say 60% health you could turn that off and just have it as a use on CD/Burst.
Consecration
Now the CR could just be very moody when it comes to this spell because sometimes I don't have an issue with it at all, well others I never see it get used... Like ever, lol. Typically its if I'm on the "max dps rotation" build that it doesn't use Consecration even on AoE pulls.
Shield of righteous
Our major defensive tool, that needs to be up almost all the time, currently the way the CR works with it is... considerably understandable ? cause I'm not sure if you could code it to work the way I'm about to suggest, but if at all possible. It needs to be this way.
Before I began using combat routines on my paladin, all forums/reading/research etc, and its how I've always done is you get 5 holy power, use Shield of the righteous, hit crusader strike, then shield of the righteous, repeat. currently in order for this too happen, you have to do the crusader strike and second shield of righteous yourself.
Adjusting it to work like the way I suggest will give the best available up time on Shield of the Righteous
Hopefully you don't ignore my feed back like it seems you have for monk (Other then the guard feed back for double guard, you actually made that change, haven't played my monk since thou)

and actually use it to try and improve the combat routine as much as possible, I'm 100% sure its more then capable of adding the adjustments I said for Holy Avenger, Sacred shield, and Word of Glory, I'm however not sure about the Shield of righteous one, but I'm positive you cam.