I want to point out that LOST is a special case, because we're not just talking about magic beans in terms of where it went wrong.
The problem with LOST specifically is that it was promoted, until the end, as a mystery. And the central question of the mystery was: what is this island and why does it make these things happen? The question of the island was the point of the show. LOST literally advertised its final episodes with a commercial that ended with a guy saying "I promise, I'll explain everything."
To not answer that question makes the show, therefore, pointless, and a violation of the promise the storytellers made the audience.
I liked the idea of a "Wonderland" movie initially, but thinking about it more I don't think it replaces the "magic beans" concept. It's more a description of the type of movie -- a "Wonderland" movie or a "Heist" movie or a "boy meets girl" movie. The magic bean is still a definable thing -- in a Wonderland movie, it's what creates the Wonderland.
In HARRY POTTER, the Wonderland is the wizarding world. But the magic bean is simply "magic is real." The Wonderland is the execution of that concept.
The thing is, that the Wonderland/magic beans still have rules. The magic in Harry Potter is never "explained," insofar as they don't make up any bullshit about midichlorians or whatever, but there are still rules, both to the magic and to the Wonderland.
In HP, one rule of the magic is that magic cannot be used to create food, drink, or living creatures.
But in a broader sense, a rule of the Wonderland is that this is a magical wonderland. I mean to say that if suddenly Hermione developed leet hacking skillz by plugging a conduit into her brain, and stopped using magic, the rules of the Wonderland have been violated because it's not a science-fiction Wonderland. And if it IS a science-fiction Wonderland, you had better be ready to explain how everything that's come before can be explained through that lens. Otherwise, as a storyteller, you're just babbling.
That's the issue that I see with what I know about LOST, that it kept changing the rules without ever explaining clearly what the rules were, why they were changing, or how they weren't really changing, they just weren't what you thought they were at first.
I think a major problem with the "midichlorian" debacle in the prequels was that it didn't actually explain anything. It didn't answer a question the audience was asking, as they had just accepted "the Force" at face value as part of their original suspension of disbelief. Changing the rules like that signaled the audience to start thinking "What you think you know is wrong," which quite honestly I'm on board with in a prequel story. It seems to me that the only reason to do a prequel is to tell us that it's not what we think it is. But he didn't leverage that, at all. He knocked us off-balance by telling us this spiritual Force was actually quantifiable and sciency...and then just kind of left that hanging out there. Never returned to it, never leveraged it, just said it for no real reason. Babbling.
Or, to make a more related-to-LOST point: Lucas teased us for years in interviews and such, that Obi-Wan's line "If you strike me down, I shall become more powerful than you can possibly imagine" was, like, the key to everything. That this was a major, important thing that we were going to understand much more deeply via the prequels. He said it was going to come into play in AOTC...and then it didn't. And then he said that it was the crux of ROTS...and then it wasn't. Yoda just has a throwaway line about "Oh, I've been chatting to Qui-Gon btw. Yeah apparently we can do that." The end. If you don't have the answers, don't go out of your way to put the questions in our heads.