I've run into a few things I thought I'd mention in working with the Atlases/Fonts...
If you have an existing atlas and you try to add a new texture to it while the packed texture PNG is read only, your atlas will get messed up. I believe it goes ahead and modifies the atlas' coordinates to account for the addition, but since it doesn't write the PNG the new coordinates are incorrect. It'd be great if the process would either do absolutely nothing if it can't complete successfully, or to handle this particular problem, switch the PNG to writable so Unity can update it.
It'd be nice if items in the atlas remembered their original source texture. I've name my assets things like "Button_HiRes" and "Button_LowRes" and pull them into an Atlas and rename them to just "Button" so I can swap the atlases out. Problem is, I can't update the assets as easily this way because nothing connects the filename "Button"HiRes" to the sprite name "Button".
Somewhat relatedly, if a widget is using a texture that doesn't exist because I've deleted it (so I can replace it with another, I'd rather it wasn't automatically reassigned another texture in the atlas. If I accidentally delete a texture, I don't want to have to dig up all the old references and fix 'em back up.
When I pull in fonts from BMFont it seems to fill the background with black around character blocks which causes the edges of the letters to pull some black from the background when filtering. It'd be nice if there was a way to tell the atlas/font builders what color to fill the background transparency with, or maybe even an option to copy the neighboring colored pixels in.
Really, any graphic does the above - I can see a solid case for not supplying a fix for fonts (really the issue is with BMFont). But, for example, if I have a 8x8 white square in my atlas the outer pixels all end up being grey after filtering. I tried fixing this by moving the Dimensions of the sprite in by one, but then when I updated the atlas later they'd be wrong again. I assume the texture packer throws out the pixels that I clipped out by modifying the dimensions since nothing seemed to need 'em anymore.
Anyway, just a few things I've run into I thought I'd note...