The current Popup Palette has many problems that deprives its usability. 

1) The color thistory blocks keep changing their sizes, and thus also their places. We don't know which one it the most recent one. This is very confusing indeed. 

2) The Favorite brushes on the Popup Palette also suffers a similar problem, when users add a brush to favorites, they don't know where Krita is going to put it on the palette. I think most of us want to control that.

My suggestion is:
1) Create a gap on the palette. This works as a indicator to show the users where is the start point;
2) Add something to indicate the first/most recent item;
3) In "Select Favorite Presets" window, add buttons to allow users to change order. A Popup Palette sample is displayed to reflect how the settings may look in realtime.

I've draw a concept image. Please see the attachment.

Reproducible: Always