Just a few ideas:
Emirate of Crete (early middle ages) is missing
Some ideas for additional Holy Roman Empire colors (especially for the South West)
Pfalz-Zweibrücken is missing (+ maybe other branches of the Palatinate)
5 variants for HRE bishopric territories
5 variants for HRE monastic territories
5 variants for HRE imperial cities
Geroldseck/ von der Leyen is missing
Different colors for Fürstenberg and Breisgau. Because easily the Duchy of Breisgau-Modena (1803-1806) could easily overlap with Fürstenberg (1664-1806) . Both territories existed at the same time for 3 years.
(
https://de.wikipedia.org/wiki/Herzogtum_Modena-Breisgau ;
https://de.wikipedia.org/wiki/Fürstentum_Fürstenberg )
3 colors for Basel
Basel-Land
Basel-Stadt
Basel-Bishopric
2 Colors for St. Gallen
Bishopric St. Gallen and City of St. Gallen (Both existed independent of each other)
Bishopric of Konstanz
Grafschaft Klettgau / Principality of Schwarzenberg
Territory of House Turn & Taxis
Principality of Hanau-Lichtenberg
Principality of Sayn
Bishopric of Münster
Duchy of Arenberg-Meppen
Bishopric of Speyer
Grafschaft Montfort (maybe double use a color from Liechtenstein, since they controlled at some point parts of it)
Territory of House Waldburg
Monastery of St. Blasien
Baden-Hachberg and Baden-Sausenberg as additional branches of House Baden? maybe