I'm personally more of a game artist, I think I've only ever made "pixel art" about 5 times or something. Not something I'm too interested in. The sprite focus is definitely good for me.
My main problem with the interface is even with the documentation, I have no idea what anything does and the controls don't respond as I'd expect, in fact at times they seem situational. I think if a little screenspace was dedicated to a tiny toolbox it would help things a lot. Another option is a sort of pop up menu like animanatee does: when you hold a key, in their case it's L, all the options are at your fingertips.
Also, sometimes when I'm fooling around with the tools to try to learn them, I get locked out and cant find my way back to drawing and need to restart.
While I pixel I'll only ever have one hand for buttons, so making the left (or right, its usually mirrored in ds tools) dpad (buttons) contain everything I'll need is a plus.
If you want, I could give you a mockup of what sort of thing would be most helpful. SEDS is much more powerful than anything else out there, it's just much harder to use.
My own level editors etc that I have made in the past are a bit cryptic and someone else wouldn't know where to start - so I definitely understand why SEDS is hard to use.