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.
I was experiencing some weird rendering issues with the editor when typing my response, I left this part until last for a few reasons but here I will answer it.
Mostly I feel that it's due to the process. Sometimes I would need a tool more than the two available through the custom tools selected for my mouse buttons which required me to bring up the "Quick menu" select a new tool, click out of the menu, use the tool for that one operation, go back and select my pencil tool again. The only way you could improve this is to include hotkeys that can be altered by the end user to couple the already really nice ideas you have here for custom toolbars and so on, this would allow users who prefer an interface and users that prefer hotkeys to mix and match their desired preferences as they see fit, which would be nice.
Alternatively you could include one hotkey that provides a context sensitive tool set for the mouse buttons, so if usually my mouse buttons where tied to "LMB - Pixel Tool" and "RMB - Eraser" then if I hold "ALT" or some other desired hotkey they the tools used on those two mouse buttons would be different and to set them when in the "Quick menu" we would just hold the "ALT" key while selecting the tool to use on those alternate buttons that are context sensitive to that hotkey.
The above could work as a nice tough without over complicating things too much and allowing those of us to alternate additional tools in a more fluid workflow.
Also, I did like that you have the colour picker that reverts to last active tool, that saved some clicking here and there, if you tied that to the alt key alone, that in itself would likely be a huge time saver for people but I'd opt for the above suggestion if you feel it's something you can implement and wish to, as it allows for a little more to anyone's workflow.