So I made dungeon mods before (Orvar's Tomb, Westbrook Keep & Wheeze's Dungeon Pack) and I discovered that alot of people who used my dungeon pack are experiencing incompatibilities and crashes. I won't go into detail about this and I am not asking on how to make my previous mods compatible. I am asking what I should keep in mind in order to make my mods as compatible as possible.

I did a little research and the just of what I have learned so far: Try to modify as little vanilla skyrim stuff as you possibly can. For example: Do not remove trees or rocks when creating an entrance to a dungeon but rather move them underground.

So what else should I look out for ?

And a bonus question: Is it okay to remove vanilla navmesh? Will that still cause incompatibilities?

Just remember that an incompatability simply occurs when two mods edit the same record. That said, edit as few vanilla records as possible. If you're doing something like adding a new dungeon or quest, you should be able to without editing a single vanilla reference. (Make all new forms of them instead) But if you were making a mod that balanced gameplay by changing how much food heals you, and how much damage weapons do, it would be impossible to do without altering the vanilla records. Therefor your mod can be very compatable, or unaviodably incompatably with other mods of the same time.

Yeah but navmesh sometimes needs to be removed in order to fix various AI problems. Can navmesh be removed without incompatibilities ?