Thanks for trying it out. :) People actually using Pixel Proof and describing their experience goes a long way toward making it the best it can be for all of us. I'm glad you found some things to like! Pixel Proof is what happened when I decided I had too many good ideas (read: experimental ideas) for graphics editors that weren't in any other editors. Over the past few months, many of these ideas have been settling down into useful (and less experimental-feeling) interfaces. However, a lot of this app is still pretty rough, with original experiments hanging around without any UI to adjust them (like the scrolling background).
Can you tell me what, specifically, you need to click a lot to achieve? I'd love to fix whatever that is, assuming it's not covered by the other descriptions.
The tool icons will definitely be updated in the future. I actually only recently did a run through them to replace all of the placeholder icons, so these are just 2nd pass programmer art. ;)
It will also help when the menu is revised. I'll be grouping tools together with spatial partitions so you can find things easier. Even bigger than that, though, will be the custom toolbars I have planned. The quick menu will let you populate the toolbars (one for tools, one for palette) and then you'll mostly use those instead of opening the menu.
I just fixed the palette hotkeys '[' and ']' so that the current palette is used. That'll be in the next update.
I recently switched to someone else's dialog library, so I don't think I have control over where the color picker appears. In the near future, though, I'll be implementing an in-app color picker instead (for several reasons), so the positioning won't be a problem.
View Mode is an experiment that might just go away, and any of its bugs with it. The idea was that the app could be used as a lightweight image viewer that could swap to editing at the press of a key (Enter/Return). I'm not certain this would be useful.
I'm still designing the palette management system. Likely, the last palette will persist, you'll be able to save palettes to some palette file and load them again later, palettes may be saved automatically (like GIMP does), and palettes may also be associated with a future editor file format (analogous to .xcf for Pixel Proof-specific needs). Palette editing, too, will be improved, as you can't even delete entries yet.
The only way to currently "move" pixels is to cut and paste them... but that needs work too! I'll add something that makes this process better.