*facepalm*
Alright, down the list.
The Kanto-Johto-Hoenn Dex Holders are currently in limbo. It's unknown where they are right now (barring Crystal, who we know to be at Oak's lab), but it's assumed that they're back home.
Ho-oh and Lugia did indeed appear already, but so did Celebi, and she popped up again. They will appear if needed for plot purposes, though it would be kind of a stretch to have them appear again.
Giovanni's given goal was to find Silver, but we don't know what for. Hopefully he just wanted to be a family, but as the Beast trio implied, he could have been looking for an heir. Either way, he's most likely in the hospital right now.
The beast trio (besides Sird) was completely destroyed.
Mewtwo will come back as a later plot device, and Deoxys stated it was heading to Sinnoh to check out the asteroids in Veilstone.
Also, the other Deoxys is in Fiore.