Ok, I've had this theory for six to eight years now, but I've mostly kept it to myself because it was just a stupid idea, and 10 times out of 10, game theories are wrong. But after finally playing Thimbleweed Park, I'm 100% certain my theory is correct. I'm going to put the rest in spoiler tags, because it contains spoilers for Thimbleweed Park (and Monkey Island 1 and 2).
Spoiler
I think the ending and twist Ron Gilbert had for Monkey Island 3, was repurposed for Thimbleweed Park.
Which is that The Secret of Monkey Island is a game. It's clever word play, because it is a game, and that's also the secret.
The usual theory is that Monkey Island all takes place in the imagination of Guybrush Threepwood, but I remember (hopefully I'm remembering correctly) reading that Ron Gilbert straight up refuted that, and also said that the actual answer is quite obvious when you know what you're looking for.
And if you think about it, there's nothing more obvious than Monkey Island being a game, Guybrush even says it at the end of The Secret of Monkey Island. And everything that could be interpreted as children breaking character (the swordfighting pirate on SoMI telling Guybrush to play along with the pirate speak), could just as easily be interpreted as game characters breaking character.
But the real reason why I think this theory is true, is because I came up with it six to eight years ago. Waaaaaaaay before Thimbleweed Park was even a concept. And lo and behold, the latest game from the same creators just so happens to have the twist I theorised for a game that they never got to make.
It wouldn't be the first time a game creator has reused a concept they came up for a game, in a completely different game. A recent example I learnt about was the time mechanic in Prince of Persia Sands of Time originally being conceived (and refused) for Donald Duck Quack Attack.
And let's not forget that Thimbleweed Park has five characters because of reusing an old idea. The whole game seems to be about reusing old ideas.
Also, it's a theory I've never heard anyone come up with before. And once again, I think I remember Ron Gilbert saying somewhere, that no one had ever come to the correct answer.
Whether or not this was going to be the end of Monkey Island 3, the Secret of Monkey Island, or just an unrelated twist, I'm not sure. But I am 100% confident that the idea came from that never-to-be-made game. And I wouldn't be posting this if I had a shred of doubt (which is why I've never once mentioned it on these forums before.)
Also, I think this would have been a terrible twist and/or ending to the Monkey Island series, and now I'm glad we got CoMI instead. (It kind of sort of works for a single game like Thimbleweed Park, but definitely wouldn't work for a trilogy) I still want to go into an alternate dimension where MI3 exists though.