I remember there being preflight cutscenes where you prep your craft and get your r2 unit prepped, and then a corresponding cutscene after the mission with crew repairing any damage your ship might have. There are also some other cosmetic changes I've noticed in between mission. Were those taken out? It's a small issue, but it kind of irks me.

Ah, makes sense... now the million dollar question: start over or just let it go?

Well... Being a Wing Commander fanatic, I'd say -> LET IT GO! I've re-played Wing Commander V this year (story sucks, flying is awesome) and got heavily annoyed when I heard "The Iceman would've been proud" for the hundreth time -.- Seeing your ship going into this "start catapult" before every mission had the same effect. You're going to skip those scenes anyway. Be glad they're "auto-skipping" ;P

Haha, that's what I'm finding. I'm already skipping everything.

there are transitions in the xwing98, too, you can activate/deactivate them in the options menu