Regarding #2
NGUI only sets a a minimal amount of settings now, where it earlier forced it to be max size 4096x4096, true color, non power of two etc. Now it only sets alpha is transparency, which means if you have it set to "Texture" it will default to Compressed (yuck) and power of two (also yuck for UI). This is cause a clear quality degradation in import - well, it will be exactly as icky as the actual imported texture is, even if the Atlas is true color.
Generally, it's a good idea to set the textures to be either the GUI preset or advanced and set the individual settings underneath as well.