After analyzing all arguments for and against, I'm seriously beginning to consider removing CoT altogether from my module in the making.
There are several things that made me think it might be a good choice.
1. Virtually no difference lore-wise between paladins and CoTs - if you showed abilities of these classes to someone not familiar with NWN or D&D and asked them which one is a paladin, they'd probably have to guess. Other classes, even when similar, still have their characteristic traits that differentiate them. Shadowdancers, for example, while proficient in hiding just as rogues are, manipulate shadows to accomplish this. Fighters have versatility that Weapon Masters lack, while WMs, in turn, are focused on a single aspect of fighting, dealing high damage. Paladins and CoTs, on the other hand, have no such notable difference. As such, I can't get rid of the feeling that CoTs do not serve to fill any niche.
2. Pointlessness of taking more than 20 paladin levels - there is virtually no reason not to multiclass once you reach paladin lvl20. Even those who want to stay as "pure" paladins most often decide to multiclass with CoT, since lore-wise there's almost no difference between the two anyway. If CoTs are removed and paladins are given their Divine Wrath spanning paladin's epic levels, levelling pure paladins will be a viable option.
3. Sacred Defence is too good - CoTs might not be as powerful by default as Weapon Masters, but they're not far behind, and the reason for this is mainly Sacred Defence. (Of course I'm not for removing any class that is too powerful, but it's still one of the arguments I have for removal of the class.)
4. My module is a non-FR one - so there's no such deity as Torm here. I could, of course, rename the class to generic Divine Champion, but then there would be even fewer differences between them and paladins, see point 1. '>
So, to sum up, I'd want to remove CoTs altogether and give paladins Divine Wrath in return. In a single move (well, two moves, to be exact) I'd make high paladin levels useful, remove imbalance in the form of CoT's Sacred Defence and remove a class that basically shares the exact role of another class.
Now, since such stuff is not just a slight modification of game rules, but something bigger, I'd like to hear your opinions on that. If you're a player, would you feel limited by having CoT unavailable to you? If so, why?
If you're a builder, do you see any other complications or downsides of doing this?
Tell me whatever you think.