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.
One of Us: Jared Pullen, the lead artist of the trilogy, has an official deviantART account where he takes questions about the trilogy and goes into detail about some of the things that didn't make it into the games proper.
Shrug of God: The creators of the trilogy intentionally left Spyro and Cynder's fate at the story conclusion open to interpretation.
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.
Jared Pullen, the lead artist of LoSdid a Q.A. on some of the stuff they never got around to implementing or building upon. This includes, among other things, the fact that dragon eggs take decades to hatch, that they were indeed considering revealing that Ignitus was possibly Spyro's biological father but were halfway split between Ignatius or Malefor being his biological father, that if adult female dragoness had appeared in the series, they would have been even more slender than adult Cynder was note Adult Cynder was apparently rough around the edges due to being artificially aged up, and that there's another dragon around Spyro and Cynder's relative age named Pyra out there, currently stranded on a deserted island.
He also later confirmed that something bigger and ''much'' more powerful than Malefor corrupted him, and that Cynder's natural element is wind and natural wind dragons exist. It also confirms that water is also a natural element in the LoS universe and that Cyril was supposed to be the female Guardian of water originally. Pure shadow, fear, and poison dragons also exist, but they aren't natural, and is the result of a "dark entity" (perhaps the same one that corrupted Malefor?).
According to Jared, Cynder joining the temple after being saved by Spyro was supposed to be a point of contention among the Guardians, with Cyril being the most vocal dragon against it. It wasn't until Ignitus stood up for her did they finally accept her. Time constraints, however, kept this detail from being known until years later, with the Guardians never stating their opinions on Cynder's return to the temple in the games proper.
The elemental wheel used to power up elements in the games was originally supposed to be an actual object Spyro would have encountered in game, but time constraints forced them axe that for the system in the games.
Word of God: As stated many times already, Jared Pullen, the lead artist of the trilogy, has a deviantART account where he answers questions about the games, goes into what they weren't able to fit into the trilogy, and further elaborates on things that weren't fully elaborated on in the games.