I've been reading the theories posted here about the origin of the Guardian and clues about changed or incomplete quests in the data files for various Ultimas. I want to compliment the people contributing to these threads that you are very observant on issues of Ultima continuity and are incredibly creative when it comes to speculating about the empty or contradictory spots in the games put out by Origin.
I was speculating about some of these same concepts and contradictions in the Ultima universe but I concluded that there's no point in trying to tie up the loose ends. Commercially, it's trapped by the fact that EA still owns and can enforce copyrights and trademarks on almost anything Ultima related. And since we're dealing with a creative work (not just code) continuing a story that was created by someone else could be just as problematic as trying to create your own Larry Totter novel that used Ms. Rowland's characters and situations even if you avoided any of her actual prose.
A much better expense of time and effort would be made by starting over with a new premise and building a new world using the Exult engine. Of course, until new artwork and sounds are made it couldn't be distributed, but the first step is coming up with new plots, puzzles, and stories. Initially of course we'd have to continue using the U7 art and sound while fleshing out the game. Kind of like those people who made storyboards for their action movie by photographing their Star Wars action figures, but with the full intention of one day replacing them when they've fleshed out the plot to fully define the personalities to the characters to know how to cast them.
How did I come to this conclusion? Here are two aborted story ideas that tried to use the Origin continuity.
My first idea was to remake of Ultima's I-III using the Exult engine. I have a lot of nostalgia for these games and despite their tiny worlds I speculated that if the plots of all three of the games were worked into one adventure (with three bad guys) using the Exult engine it'd lend some size and complexity to the game while allowing one rewrite some of the incongruities and even make the whole exercise of a little less monotonous in that you'd only have to do it once for all three adventures

After thinking for a while, I concluded that it'd be more workable to have a game from the perspective of a noble young apprentice named Mina Xavier. She's a computer programmer summoned from our world by an older, powerful man. It's a world of chaos and magic, but he's worked hard to begin bringing order to it. His methods are ruthless and not terribly compassionate, but it's a noble goal to bring peace to this fuedal, warring world. As you've probably already guessed this would be a new game, heavily influenced by the plots of Ultima I-III, but told from the opposite perspective. Indeed, one of the Lords (also a summoner) would be described as being so ruthless that one dare not speak his name (for copyright reasons

I like this kind of plot that takes a well-known, simplistic story and fleshes it out from the opposite perspective (like Gregory Maguire does in books like "Wicked" and "Mirror, Mirror"). It's also refreshing that it ends by choosing to loose the "big battle" rather than decimate everything. (I'm not sure that such a thing could be techncally done in a manner as satisfying as the "kill all things" games). Overall though, it still smacks heavily of a derivative work. Admittedly if no names or copyrighted material was used from the original it might be okay, but it'd be depressing for a bunch of lawyers to be called in to fight out the question: is it derivative?
I've no misconceptions that the biggest goal of Exult is to get Ultima VII working with a non-Origin engine. But in terms of creating new work with Exult and Exult studio the only sensible thing to do is to drop the continuity and names from Ultima and just start afresh. I'm not at all experienced with usecode yet, but it looks comprehensible and usable and having some ideas for plots might give me more impetus to develop small quests that can be woven into a larger story.
Let me say again that starting afresh isn't a bad comment about the worlds that Origin created. I really enjoy playing the exisiting games and get a nostalgic kick out of looking over the maps and books that created that rich playing environment. It's just that legally the continuity that's been built is either extinct or will be developed further only by EA. Letting it go is really the only option.
So enough rambling. What's a good plot idea? Well, this response has already gotten far longer than I anticipated so I'm going to put my thoughts into a followup about a backstory for a new game. If you have other ideas for different backstories I'd encourage you to also post followups or other threads. Maybe bouncing ideas off of each can come up with something nifty and challenging and worth the development effort that's a worthy equal of Ultima VII.