How to change the color scheme in KeyNote 6?
By looking at the images you’ve posted it seams that the second palette is obtained by opening a PowerPoint presentation via Keynote: the arrangement of the dark to light shades/tints is opposite and the shades of white-grey-black at the bottom of the palette are quite different.

I assume that you have to create a palette in PowerPoint (the so called Accent colours), save the presentation (it can contain a single blank slide) as .pptx. Then open it with Keynote and save it as .key file.

The original Accent colours (i.e. the last six colours that appear in the first raw of the colour palette in PowerPoint - for example when you want to change the fill colour of some shape) in the Keynote's scheme colours will be placed in the second raw. Now you have a brand new palette to work with. Just check the Master slides in the converted presentation (personally I don’t like the "conversion") and modify them (if necessary).