Personally, I like having the choice! Which is why the PNG Atlas tool is so critical, in spite of its rough edges -- because Unity currently doesn't let the developer choose easily, and instead always opts for speed over package size. Which is great on PC... but on mobile, it's almost always the wrong choice.
I made a post on the Unity Feedback system endorsing a native implementation of such a feature:
http://feedback.unity3d.com/suggestions/png-and-jpg-texture-formatPlease go vote on this issue!
Using PNG Atlases brought our package down from 800MB to under 200MB... we're going to release a big game for mobile no matter what, but it can't be in the GB range. But it should be even smaller -- a number of our textures, including stuff we aren't using 2DToolkit for, or stuff we're using in conjunction with the Spine animation system can't be easily compressed.
Native Unity support for PNGs is the best long-term solution and people should feel free to make some noise about it