Okay with let me just explain why I think the Rakatan will win because this is going in circles
- We know that the Ratakan have a billion force users that use the Dark Side of the force and know what the force is. It would be logical for them to actually use force techniques.
Especially when you consider that the elders recognised the techniques Revan and Malak used as the use of the force. They would probably not do that unless they had a good understanding of it. And that is after god knows how many years of war and losing information and not seeing the force being used. I mean seriously the Rakatan would have to have a great understanding of the force, and by all logic be able to use the force quite well.
If the Rakatan understand the force which they do. Then they would have been trained in the use of the force for a very long time. And they would train their children with the force because they were all force sensitive, at least at the height of their Empire. After that the plague started appearing they started losing their connection to the force and they lost the power to control the Star Forge.
On the Star Forge, we know that people more powerful then DS Bastila (In Kotor II), who when much weaker took out a Dark Jedi defending Revan, were not powerful enough to control the piece of shit.
So its very likely that the Ratakan know force techniques and were quite powerful to control the power of the Star Forge (More powerful then Kotor II DS Bastila at least).
Now the most powerful Rakatan would have been more powerful then Bastila and would know force techniques.
Now of course it is possible that the guy was just a bit more powerful then Bastila and all the rest was a lot lower then that, but that just sounds so incredibly stupid. You do not create a warrior race who's only purpose is to fight and enslave without training your warriors. Just think about the Mandelorians, these guys were the greatest around because of their training. The Rakatan are a warrior race, and a warrior race is trained from early on. The Rakatan would by all logic control the force quite well and be quite experienced with it.
So seriously, you can argue this but its very likely that the Rakatan had a lot of powerful force users. And quite a few more powerful then Bastila seeing as they survived for many years and had several leaders that controlled the Star Forge.
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The Empire for that matter has the technology and numbers for this war. But against force users a fight is going to stay hard... No matter what, the Rakatan would just have to start playing like the Rebellion. Keeping the unknown world as base.
The Star Forge could only be destroyed by one weapon and that weapon can be taken out by one single noob force user, the Rakatan are very likely more powerful then that they could take out the Death Star. The other Death Star just orbits above Endor doing absolutely nothing and only becoming dangerous when attacked.
Now of course Thrawn is a military genius, and unfortunately I never read any of his books, but is he able to fight a guerrilla war. Its a completely different war then anything he has probably ever fought although I have to admit i'm not sure about that. Even if he is he's still going to face force users, and that is he is going to be put in command of anything important. Afterall he wasn't in command in any of the most important battles the Empire fought (Yavin, Endor). So why would he be here?
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Now on the technological thing.
You say the Sith did it, this is of course possible but unlikely. If Revan would have put the design for his robes in the Star Forge then why would he have put a lightside version design in the Star Forge? It makes no sense he isn't on the light side. And if he did which is just really really really strange and not something that a smart person let alone stand Revan would do. And why if he did put the designs in the Star Forge was he the only one that used it.
It would only be logical if the Star Forge analysed the clothes Revan wore the first time and would then use the force to recreate it when Revan asked for it. This seems to be the only logical explanation there is.
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And then you have the obvious ramming option. Create a droid, create a ship let the droid fly the ship and bam there you have it. No more SSD. I mean this could very well be done. Especially if the Rakatan manage to steal an Star Destroyer and use that technology instead of their own. SD's have hyperspace travel without the force. Probably slower then that of the Rakatan with the force, or maybe just as fast because of new technology, fact remains its going to do a lot of damage.
This isn't going to be a normal war. This is going to be completely different in all regards. The Empire will win if all they have is suddenly dropped into one system and the two will have to face each other. But thats not going to happen.