why is it that in the NWT there are certain phrases that have caps while others do not?
Not sure what in particular you are referring to without examples.
I think you might be referring to a couple of things:
1) Places where YOU appears in all capital letters.
This is the method of the NWT translators to explicitly indicate when the pronoun "you" is plural. In virtually all languages besides English, there are distinct words for you-singular vs. you-plural. In English it's just plain "you" in both cases. So when you read "YOU" in the text you know it is plural.
I'd say in well over 90% of the cases the context alone would be enough to determine whether the "you" is singular or plural without the capitalization. But as you noted, the WTS is often quite anal about insignificant matters, so it is what it is.
2) Places where a pronoun is capitalized
This is typically done in cases where the antecedent of the pronoun is ambiguous - by capitalizing it or not, you can indicate which antecedent applies.
For example, suppose you said "God told Abraham that his patience would not last forever". Does the "his" refer to God's patience, or Abraham's patience? It could be either.
But if you wrote "God told Abraham that His patience would not last forever" then, by capitalizing the "H", you indicate that the "his" applies to the "greater" of the 2 persons listed. In this case, the "his" pertains to God.
they do not copy the same style as those writers of old.
I don't understand your issue.
Why should the writers of an English translation follow Koine Greek grammar or punctuation rules?