My quest writing for Morrowind had my inner critic pop up. My quests for an upcoming mod are pretty good, compared to my last efforts in Desert Region 2/Ashes of Apocalypse. But my Oblivion mods had full fledged dialogue trees. Oblivion's CS made it a lot easier to make them, but Morrowind's Choice function seems very unwieldly in comparison.

Are there any tips on organising dialogue trees in the CS, so they work efficiently?

I usually have a rough outline of all the Choices on paper. Just so I can see where each answer leads so I remember to make sure they are connected in the CS.

I also usually find mistakes while testing, so I think a bit of trial & error is common since Dialog is not exactly user-friendly.

And always remember the top-to-bottom rule. Keep your Choice outcomes above the Choice itself.