Ironically the Star Wars Battle of Endor does NOT suffer from BoE Syndrome. The syndrome is so named because people were trying to recreate the Battle of Endor they loved in Return of the Jedi in FS1 (and FS2) and failing miserably at it. The real BoE is an example of a BoE mission done correctly. Assuming the player is in control of the Millennium Falcon he has clear cut objectives, the results of which do have an effect on the storyline afterwards. In this case they actually affect whether the rebels win or not but this is incidental. What is important is that the player has objectives, and they matter.
On the other hand if you place the player in the seat of some random X-Wing fighter outside the Death Star then there is a very good chance you'd end up with BoE Syndrome.