Desertion of the Dinobots (1) - S2-E19
Plot hole: Perceptor discovers that the reason for their malfunctioning is because their Cybertonium has deteriorated after millions of years of being exposed to Earth's atmosphere. The key word here being 'millions'. This explains why the original Transformers who crash landed on Earth (4 million years ago) are affected, but newer characters like Perceptor, Powerglide, Hoist, etc. are affected despite the fact that they have only been on Earth recently.
Plot hole: Omega Supreme transforms his arm into a rocket and blasts off to the moon, but later, he transforms fully, but he left his body on earth, how was he able to transform?
Plot hole: When the Quintesson scientist is tricking Cyclonus into going inside his ship he disguises it as a character named Broadside who then says that he has come to take Cyclonus to see Galvatron. The problem is, Broadside is an Autobot yet Cyclonus simply walks inside without any reaction. Most likely the writers intended it to be Astrotrain but wrote the wrong name down.
Answer: It is whichever ending you want. There is no 'real' set or canon ending to the war. The only semi-resolution is Beast Wars occasionally hints at the Autobots winning (before the Maximal upgrade). However, Beast Wars is a combination of the US cartoon and the US comic, and excludes most of the Japanese continuity. So it is really up to you as to what you want to believe. Most people seem to 'accept' the US universe, ending with Beast Machines.