As far as I know from Cocos2D 2.0 a 1025*1025 texture does NOT use 4 times more memory than a 1024*1024 texture, just proportionally more.
If I put my textures to an atlas, there is some unused space almost all the time. This is wasted. (Not to mention the iOS5 POT textures memory bug, which makes POT Texture Atlases waste 33% more memory.) But If I just use my textures the way they are, then there is no memory wasted. The only advantage of Texture Atlases in my opinion is the ability to use a SpriteBatchNode. But my app is heavily memory limited, and I only support devices which support NPOT textures. I know that NPOT texture handling is a bit slower, but saving memory is the most important for me.
I might be wrong, please confirm me, or show me why I am wrong. Thank you! :)