This discussion was brought up quite a bit last year on how large the new window is in Krita. These complaints are recently starting to come up again more (not related to the clipboard bug it seems). Here was the previous discussion on the direction.
https://forum.kde.org/viewtopic.php?f=288&t=125225&hilit=UI&start=15
The design direction left off with this direction. http://www.scottpetrovic.com/uploads/krita/ui/march/new-dialog-update-v3.pdf
The custom document window would look like this... http://www.lyzo.eu/f/20150310/krita_newlayout.png
We now have a color model chooser button in the custom document, so that will need to get added.