2 hours ago, micheldebruyn said:1) The Republic didn't have a military.
2) The clones fought on the side of the Republic.
3) Clones weren't mentally unstable.
4) All clones had the same progenitor.
5) No insane Jedi clones with oddly misspelled names.
1. I'm not sure what exactly you're referring to in this, I cant see how this can be a contradiction. The prequel trilogy demonstrated a Republic with military in the Clone Wars and a Republic without military prior to it, so whatever the EU writers said about the military or lack thereof, its probably fine.
2. Score 1 point for a legit contradiction. However, references to the clone wars from the early EU are vague and few in number, so fixing it only requires you to change a handful of sentences and never really comprimises any major plot points in those stories.
3. Two different types of cloning are at play: Kaminoan cloning and Spaarti cloning. Call it a retcon if you want, but it makes sense: different methodologies have different results. Calling this a contradiction is like saying that the existence of cell phones contradicts the existence of desktop computers.
4. Kaminoans used one progenitor because they thought Jango was the best and anyone else wouldnt be as good. Its not like they were unable to make clones of other people. More diverse clones became popular later on, probably to specialize in different tasks... but so what? It's just like 3: a different use and approach to cloning.
5. I'm not sure why the clone Joruus C'Baoth's backstory was never explored, but just because the movies didnt mention them doesnt mean he doesnt exist.
Yes, it's true that Lucas was not perfect when it comes to creating cohesive lore, but for the most part, the aparent contradictions were either eliminated with supplementary explanations or by making miniscule edits to the prior books, and they are few enough in number that they dont come up often. So long as you keep an open mind to these explanations, both sources can coexist.