The GIMP developers will very likely keep doing things the way they have been doing them. I cannot take the GIMP seriously in terms of usability when I get that kind of response because I'm not convinced a huge amount of thought went into why things were done that way in the first place. The GIMP could be helping to lead the way but at the moment it is playing it safe sticking with what they have. Which is fair enough except that other projects have followed the GIMP based on the assumption that they know exactly what they are doing.
I know what you mean. When I open up PSP, all my palettes and such are exactly where I left them when I last used it. When it comes to the GIMP, Inkscape, etc, each palette is a seperate application, and I have to open them and move them each time I use it. Gets tiresome when Ihave to do this after a crash, etc. Right now that's my only complaint against Inkscape & sodipodi. I think if there was an open source implementation for palettes(instead of separate mini-apps) and a nice MDI arch, well, there would be much rejoicing.