Continuity mistake: Optimus Prime, whose primary color is red, when being tied to a rock alongside his troops during the episode's climax, turns blue for a second.
Continuity mistake: After the Decepticons dig up Skyfire they look at his memory banks to show what happened to him. In the flashback it shows Starscream transforming into his Earth jet mode which he shouldn't have had because it takes place before they all crashed on Earth.
Continuity mistake: Skyfire's Decepticon symbol changes color throughout the episode. Sometimes it is purple and sometimes it is red.
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.