Flashback with the Other Darrin: This happens during the intro sequences for The Eternal Night and Dawn of the Dragon. The Convexity flashback for The Eternal Night was redone with West and Whitman re-doing the respective lines for Spade and Summer in A New Beginning, and in the intro sequence for Dawn of the Dragon, Ricci re-did the "Spyro, stop!" line from the ending for The Eternal Night.
Deleted Scene: One of the planned scenes for Dawn Of the Dragon would've explained how she got her jewelry back, which she hadn't had prior to being frozen in time. She was meant to put the jewelry back on in a cutscene in order to remind her of her past deeds. There wasn't enough time to make this scene.
What Could Have Been: Just look at the art galleries in Dawn of the Dragon. The scenery gallery shows far bigger and detailed levels, and several dozen scrapped ones.
There also could've been a movie series based off the trilogy, but it was canceled due to Activision's decision to go with Skylanders. Oh, well. Perhaps it was for the best, considering most Video Game Movies Suck.