Clive, Joshua, Dion. Are they dead?: My answer is I don't think any of them are dead. Lets begin with the most obvious proof that at least one survived; the book. Who wrote Final Fantasy? I think the most obvious answer is that it is Clive. He narrates the opening and the ending of game and really only he could tell the full story. Why is Joshua credited as the author then? It has been shown multiple times that Clive has no problems with adopting other names: He is the First Shield of Rosaria, Wyvern, Cid, that one name he used in the Dhali quest and now Joshua. What about the petrification? Both Cid and Jill have various patches of petrification. Also there is the quest by Harpocrates in which he encourages Clive to pick up pen once all the fighting is done. If you pay attention to all the final character quest they all seem to imply future events. Clive definitely is not dead.
Could it be Joshua? We know he died, but is he dead? I think not. Clive brought Joshua back. How? Clive got the powers of the Phoenix from Joshua right before Ultima. Phoenix does not have power to bring the dead back as stated by Joshua but wait! After Ultima was defeated Clive absorbed all of his powers as well in a sense making him a god or at least something on Ultima's level(Likely surpassed). We know that Ultima created humans and we also know that Ultima was draining Valisthea of its Aether to cast Raise to bring back his entire race. Power of the Phoenix + Raise = Rebirth Flame, Phoenix's classic ability. Now I was thinking what if Clive's petrification of his dominant hand got so bad that he lost the ability to write and Joshua gathered the all info and wrote it for him before Clive really passes away by natural causes. Again, a quest with Harpocrates implies that Joshua is excellent at chronicling information. I also think Joshua would be the main character in a sequel.
In regards to Dion; His death is never shown. In anime that is a dead giveaway he his not dead. I also think he will be important in potential DLC/FF16 -2
Royal Meadows structure: What is this is thing? It is not some form of environmental decoration. When you first visit the Royal Meadows, there are NPC's that that comment on it, '"A wave frozen at its crest" or something like. Towards the end of the game it will be revealed that the bard in Northreach is actually an Undying and he has been sent to the area to investigate whatever it is after the previous members did not return. If you look in its direction and check the map, you will be looking into the blighted Northern territory. Originally there was 13 crystals in Valisthea and by the beginning of the game there are only 8; One of those was Drakes Eye in the Northern territories. "It collapsed into the sea" apparently; It does look like it fell over. Why are previous Undying being lost to it?
Possible Airship: The blighted area between Eastpool and Phoenix gate has a fork that leads to a door that is never accessed. On first visit Clive will mention it being some kind of Fallen structure(duh) and later in the game he mention it looking like the door to airship and wish knew how to get in. Mid's last quest had her wanting to build an airship.
Leviathan the Lost: Leviathan is mentioned once by Joshua when investing the Circle of Malius mural. Apparently, Leviathan has not awakened in a very long time. At first I thought it was because the Dzemekys Crystal was destroyed, but that can't be the answer because both Drake's Eye(Shiva) and Drake's Horn(Ramuh) have long since been destroyed but they have still awakened, and that is even assuming that Dzemekys crystal is even Leviathan's crystal. A Fan Theory is that we may already know who Leviathan's Dominant is:
She gets a decent amount of screen time for only being a NPC. She does not get nae revealed into late game and its "Kihel", Born of land of the waters. Also back to the Circle of Malius mural, you notice that all the Eikons are arranged in way that represents their relationships.
Leviathan is right next to Bahamut. This is why I think Dion is not dead.
Star of Metia: Again, something mentioned but never explored. At the end of the game the star goes out after Origin's destruction. Some will say Clive's death but I doubt he's dead. I think it was some type of satellite and FF14 players only further that conclusion. So Omega from 14 has similar origins to Ultima from XVI. I read up on it and yea! They are similar. There is also a star that poses as satellite as well. What does it mean?
Southern Countries: We are made aware multiple times that other land masses exist outside Valisthea. We know nothing about them other than they trade in Bearers and the crazy Ultima cult was there for awhile before returning to Valisthea.
Secret Order: Guys who are trying to keep origins of Bearer enslavement(History in general) from the masses. They show up but are never dealt with. I could see them being antagonist in a FF16 - 2.
I'm still obviously thinking about this game :). Lets discuss!