"Everything is an expression" is probably the general characteristic that I most love in Mathematica.
And then Images were born... The need for a different way to treat these "huge" objects was pretty obvious. The solution, in the case of the Images, in my opinion, was proven acceptable, but I wonder which other solutions were on the table.
And then Associations came, and a feeling that Mathematica had just developed a taste for Atoms... But I remember hearing someone say, when Association were live announced, that, "for now", Associations were Atom, but that it was still a possibility of making them non Atom on future releases. Not sure if that was meant as an implementation or as a global behaviour. But now that the new technology is being built on top of these structures, I guess that that option is probably out.
Besides the obscure nature of Atom structures, which I think goes against Mathematica "brand", they tend to become incomplete and messy on the edges. So, I'm completely with you. A solution is needed before it gets out of track.
Cheers,