For example if you kill falco so he isn't in the second level, when you meet the boss he'll let you take down some of his shield and admit defeat. Then surprise you with an attack shouting 'If this does not work!'.
I thought that happened regardless of Falco being there or not.
Interestingly, I gave the game a whirl about a week ago, wiping out my crew in each level--and it looks like casuallyhardcore's bang on the money! I'd long forgotten about the alternative dialogues you could get when certain members of your squadron were felled, such as Pigma's alternative spiel when you touch down on Fortuna without Peppy.
Upon reflection, I do recall that these alternative speeches were one of the most compelling aspects of the game during your first few efforts to complete it. Once you become a more seasoned pilot, you become more accustomed to the advanced routes, and fewer of your allies are defeated. The unfortunate consequence, I suppose, is that it's possible to miss several of the more obscure pieces of speech generated by more specific variables--such as a particular downed pilot, or taking lesser routes. Even some events
, like the appearance of certain Star Wolf members on Bolse, rely on what you did earlier in the game--a really engrossing touch, especially if you let one of them slip on Fortuna.