Firstly, I have to say this is an excellent mod. Very well done thematically. All the civs are great.
But . . .
I have this problem. I can't seem to wrap my head around the strategies needed to win. I am a long time player of FFH where I play at Monarch - Immortal depending on how much of a challenge I want.
I have played several games of Dune Wars on ** Noble ** and I am still having trouble.
- All of the hard counters make it very difficult to take cities.
- Most of the siege requires Nitrates? and if you don't have this resource you are never going to take cities.
- Spice monopoly victory is extremely difficult to achieve. Basically this is a domination victory. Even spamming spies to kill enemy spice harvestors won't get you the win unless you own half the map or more.
- I have lost to the AI several times now via transformation victory. Mostly the AI doesn't even have to do anything. Just get a decent amount of land to begin with and then win 250 turns later. I think the percent needs to be raised to 5% at least.
- Those spammed Mahdi units from the Fremen and Bene Gesserit are extremely annoying to counter.
All in all, unless you go for an early rush and wipe out your next door neighbour, you will have a great difficulty dislodging an entrenched enemy due to all the hard counters that they pile in their cities.
So either you win by transformation yourself or else early rush.
Tell me I'm wrong and that I just suck at the mod
Then please give me some good hints to win other than by transformation. 
But . . .
I have this problem. I can't seem to wrap my head around the strategies needed to win. I am a long time player of FFH where I play at Monarch - Immortal depending on how much of a challenge I want.
I have played several games of Dune Wars on ** Noble ** and I am still having trouble.
- All of the hard counters make it very difficult to take cities.
- Most of the siege requires Nitrates? and if you don't have this resource you are never going to take cities.
- Spice monopoly victory is extremely difficult to achieve. Basically this is a domination victory. Even spamming spies to kill enemy spice harvestors won't get you the win unless you own half the map or more.
- I have lost to the AI several times now via transformation victory. Mostly the AI doesn't even have to do anything. Just get a decent amount of land to begin with and then win 250 turns later. I think the percent needs to be raised to 5% at least.
- Those spammed Mahdi units from the Fremen and Bene Gesserit are extremely annoying to counter.
All in all, unless you go for an early rush and wipe out your next door neighbour, you will have a great difficulty dislodging an entrenched enemy due to all the hard counters that they pile in their cities.
So either you win by transformation yourself or else early rush.
Tell me I'm wrong and that I just suck at the mod
Then please give me some good hints to win other than by transformation. 
. I normally play at Emperor and give the AI a run for it's money every time. A few things to remember about war, don't always obsess about siege weapons, if you can get stronger melee units before the enemy has good enough city defenders to counter them, maybe strike where the enemy doesn't expect it first, you can take cities without the siege weapons. Use the mobility of transports to your advantage. Of course siege weapons are nice if you can get them too, just don't fret if you can't, they typically play a smaller role here than in BTS or most mods
.
. I'd think this is based on a percentage of the total spice on the map, but haven't looked at the code. 