See, those are the things I have no problem with, the coloring being more metallic, the NX-like nacelles, both very nice updates that make more sense for higher quality TV screens.
The torpedoes came out of that area on the bottom, as did the phasers, so no reason not to add those details, again, because HD. You would never have seen those torpedo tubes (or the phaser banks) in the late 60's, so no reason to have them there.
Some things literally had to be changed/added because that level of detail has come to be an expectation. Whatever went on with the pylons, that's another thing.