So, I assume the reason this is not already implemented is that it would not be feasible to paint with transparency. If that's the case, why not do the the way games do it? (I think)
Once @guiedgui's RGB color picker and/or my palette maker is implemented (linked in the replies of his ticket, you could have an option to enable transparency, with specific RGB/hex color values pertaining to it that would be converted to transparency once the image is saved.
I'll have to look into the Nintendo DSi Browser's implementation of the canvas. I remember that it only implemented about half of the canvas features, so there may have been a reason why I didn't add transparency. (Or maybe I didn't know compositing functions existed in canvas at the time.)
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