First of all, I think you're selling yourself short on the development slow down. I think you have prioritized fixing some of your early mistakes and that has benefited all your users. (Not being able to nest was my biggest gripe with NGUI before).
Right now I feel like I can do most things with NGUI, except optimize it for all my use cases. I'm not sure what the anchor / stretch system redesign will entail but I hope it will focus on getting rid of the reliance on Update methods. There shouldn't be any reason for GUI to update every frame unless it is tweened. UIGrid should be updated to the standards of the other widgets - It should contain pivot, size and reverse direction. Kind of like a label in that regard.
Recently used Assets (for selecting atlas and font) is just tedious to work with, because I don't trust it. It is not always updated and so I don't want things to break so I manually find them myself instead. Theres a little circle to the right of an Object field, but for some weird reason this doesn't work. Make that work instead of having to rely on a custom editor to locate your assets.
I think NGUI options should move over to Edit/Preferences and then have an NGUI tab there. It would be handy to be able to toggle features on and off etc.
http://docs.unity3d.com/Documentation/ScriptReference/PreferenceItem.htmlThe Atlas Maker needs an overhaul. Or maybe you can just support the new sprite system that came with the 2D update? Anyways, right now theres several issues with how it works. The "Save/Update Atlas" button should be the only button that updates the atlas. Creating a new atlas should prompt you with a save dialog instead of creating the atlas in what seems like a random folder. Adding textures to your atlas should be done with drag and drop from the Project View (or context menu). But the atlas should not be updated until you press save/update. You should also be able to see the textures in the atlas maker, like you do when you select a sprite. Deleting textures from the atlas should happen when you press the x, but it shouldn't be updated to the atlas until you press save/update.
It would be handy to have a some more context menus in the Project. Like when I have selected a textAsset and TextureAsset I should get the option to Create->Font which launches the font maker. Also when you select a texture and right click you should be able to add to -> and then get a list of all atlases in your Project. This would then open the Atlas Maker.
I also feel like how to support different resolution sizes could be made smoother. It makes sense that I have to create a font that I call "Header Font" which is a reference to "Header Font SD" and "Header Font HD", but right now the references can quickly become many and its not easy to maintain which is which.
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