Much props for the awesome placement of the StarLancer mission. It was SOOOOO hard and playing through that initial several minutes every time was annoying, but so satisfying to win.
Death of Shadow. Yeah that hurt. But for Wing Commander 3 I'd have gone with Battle at Kilrah. Especially if you had earlier let the traitor go, because you get another shot at him there. Plus, like the StarLancer mission, cap ship battles in Wing Commander were awesome. Torping a capital ship was always satisfying. Seeing all those systems go out and go red, then watching it start to break up.
Booooo for the console Rogue rail-shooter. The X-Wing & TIE series on the PC had dozens of missions better than anything on-rails. From the "historic" Redemption Scenario to the Battle of Yavin to the Golan in Alliance... everything (well, to me anyway) was way better than anything in the Rogue series. Hell, my favorite on rails Star Wars game isn't even a Rogue game. It's the vector graphics arcade cabinet.