The only reason I restart missions is because I want the satistfaction of getting bling, (or sometimes because I like to try to keep Alpha 2 alive just for fun) and because major losses and victories for the GTVA are on a single story arc, with only minor variation, not a more open-ended one. If, for instance, you could screw up bad and you'd have to play a different mission set based around correcting your screw up, that'd be way cool.
Example: You let a destroyer die (not one on which the entire plot hinges, one of the "supporting actors"), it makes your future couple of missions harder because you don't have it's support, therefore more badies because they aren't off battling the destroyer fleet you let die; and less friendly fighter escort or supporting bomber wings to accomplish the same goals.
You could also get rank pulled for really bad F*ck ups, etc. It would improve replayability too. Anyways, just ideas for future campaigns or if V/Interplay/THQ get wind of this and n(ever) stop *****ing about licensing and just make FS3.