Personally I removed the Amazon apps, NFL mobile, Imdb, slacker and other bloat too, plus VZW stuff. Some of the Roms remove the Samsung knox stuff as well, or at least disable it, if it's not being used, just check the rom intro to find one that works for you.
But honestly loved this phone even with it all stock. I just wanted TIBU backup, flashing options and... Well, options. The Note 3 is an incredible device all by itself.