TIE Fighter/WMG

The events and portrayals in TIE Fighter are more historically accurate than those of the movies
Think about it: the Rebellion sure lost a lot of stuff between Hoth and Endor and suffered major setbacks from an already depleted fighting force. Not to mention, unlike most other portrayals of the Empire, the Empire is actually shown fairly realistically, in that they actually act competently. Therefore, the Rebellion was effectively wiped out prior to Endor, and even with the Empire's defeat at Endor, were unable to muster a significant force to capitalize on their victory and was soon finished off.

The Enemy Civil War between the Empire and Zaarin gave victory to the Rebellion
Alternative theory to the above: the Empire had suffered severe blows in production capacity and leadership when Zaarin decided to stage a coup against the Emperor. This created a massive power vacuum that the Rebels were all too eager to take advantage of, allowing the Rebellion to ultimately win.
 * Although when you take the expanded universe, up to the Legacy comics, into account, it seems pretty obvious that the Rebels never actually "win". Yes, they get to form a republic, but the Empire, now astronomically more benevolent, takes them down (of course, then another civil war occurs between the real emperor's supporters and the Sith Usurper's supporters so there you go, the Star Wars universe lives up to it's name every second of every day).

Emperor Palpatine allowed himself to be captured by Zaarin's forces
This is Emperor Palpatine we're talking about. As in, most powerful effing Sith Lord ever. (Except for Darth Revan, of course. *g*) One, he is a Chessmaster ("Everything is proceeding according to my designs."), and probably plotted the whole thing. Two, he can throw frigging lightning storms at people. This is the guy who beat Yoda to a standstill. It probably was him - after all, the matter was an excellent test for Maarek Stele, and it proved without a doubt that Zaarin was plotting against him. Now he can casually send the former after the latter, and get back to important matters, like what color curtains he should have in his new Second Death Star throne room.
 * It's more likely that Palpatine was caught off-guard, so his capture was legitimate. You have to remember: he may be the greatest Sith Lord ever, but only like 20 people in the galaxy know that. All everyone else knows is that he's a scarred old man with a lot of political and military power. So he plays on that. When the men intercept his ship, he "allows" himself to be captured (using the Force to persuade them that they should capture him rather than kill him outright). He would eventually either be rescued (thus preserving his image as weak old man) or he would be brought before Zaarin. And Zaarin would very quickly find out how bad of an idea it was. And by "very quickly", I mean "over the course of several hours of horrific Sith tortures". And I'm pretty sure that Palpatine still had that lightsaber up his sleeve, just in case things got dicey. Or needed to get dicey ;)
 * No kidding. Unless that shuttle was crewed by clones of Mace Windu, nobody on that ship is living one second after Palpatine decides to stop going along with the gag.
 * There's been a lot of speculation on it. The canon explanation is Palpatine was briefly incapacitated by Arden Lyn, an ancient Proto-Sith that was serving as his Hand. It's possible that Zaarin could have gotten hold of Timmy Zahn's force suppressing lizards or a Universal Energy Cage as well.
 * Alternatively: Palpatine is old. Zaarin just caught Grampy Sith during a nap.
 * Palpatine doesn't sleep. Oh, and Palpatine is the most powerful Sith Lord ever. It's only been *wanked on-and-on* in about six different canonical sources by now.
 * But the most powerful sith EVER according to legend was killed by his apprentice in his SLEEP, but that's just going from episode III..
 * ...and that apprentice was Palpatine.

Thrawn and Zaarin are bitterly fighting each other only because they're the Star Wars universe's One True Pairing
Think about it, why else would they be going at each other's throats like that? Now if only Thrawn remembered to tell Zaarin about the hyperspace instability caused by the cloaking field.....
 * Alternatively, the TIE Defender and Missile Boat are the game's One True Pairing.
 * No way man. The Missile Boat rides alone!