If I may bring on my opinion...
About the civs
The Fremen shouldn't have Muad'dib as chief.. Unless you want to make an "historical" scenario and not a epic mod. Maybe Muad'dib should appear as a tech "Muad'dib Leading", leading to "Strange Fighting" or others advantages.
One of the trait should be Agricultural, so they can make the most of their desert homeland.
I don't know about the Ix faction. Sure, they would bring some diversity, but I'm not sure they're enough idea about them to make them a viable and different faction. Perhaps you could put it to rest for a while and concentrate on the others factions.
You didn't really spoke of the Tleilexus. They should be in the mod in a way or another.

I think they would be more appropriate than the Ix faction. After all, they are more present in the books.
The Guild should
not be a faction ! They would interfere, but they are so certain of their importance they wouldn't really enter at war, or colonize Arrakis. Keep them as Tech or Wonder.
I would stay away of the Factions from the prequels (or anything from the prequels in fact

)
About terrains
How do want to implement it ?
Only deserts ? Rocks ? What do you do with the coast/sea/ocean tiles ?
How do you keep the worms from getting on the non-sand terrain ? (Wheeled would only works as long nobody builds road on the non-desert terrains.)
Plant vegetation
Fremen should be the only one to have the "Plant forest" or "Plant Jungle" capability. Representing their will to turn Arrakis into a viable planet. Others House would not want to jeopardize their unique resource of Spice for a bunch of trees.
About the inspiration
Your main inspiration source is Dune 2000, who's basicly a remake of Dune 2 with prettier (and sometime dumber) graphics.
What about the books ? The Frank's books should be a must, at least the first three (or first two, edition varies). They would bring more deep, as the various games only focus on war and forget most of the social and technology ideas. I would pass on the prequel, as I didn't like them at all and they're contradicting with the originals.
Dune : Emperor ? I didn't play this game, but I saw some interesting units of a website. Buzzsaw being one.