For one thing a new reader would not be dumped back at the start of the story when they tried to click on a later chapter.
dingsdongs already worked that one out under the default game mode proposal.
Instead that chapter would simply assume certain choices have been made. So say someone clicks on a chapter half way through a story and lets say across the whole story there are three flags The writer would set the value for the flags (In this case lets say True,True, False) and since the reader has skipped over the chapters that let those values be changed it will spit out the "default" chapter.
It would be consistent since the values are set as soon as the chapter is entered. The game mode checks for changes before sending anything to the reader so they would only notice a change if that chapter had a change in it but that would not matter since the reader is jumping in at any point. So if a reader jumped in at a chapter that changed a True value to a False then it would just roll with that. if they then went back to the first chapter it would also not matter since whatever changes where made in that chapter would the change made by the later chapter.
What if the conditions of the thread require numeric values instead of simple Yes/No checks? It means a writer now has decide which version of the thread they want to be default and set the value of the variable in accordance with this choice, something the site is already doing anyway without the writers help. On top of that, they have to keep it in line with the other default chapters to be consistent. Otherwise, even under your simplistic example, we go from a "Yes, Yes, No" thread to a "Yes, No, No, Yes" thread, thereby destroying continuity. And you still haven't addressed what happens with multiple branches reconverging at linked threads, where this default value system crumbles due to the multitude of choices that could have been made before.
There's either a continuity-minded game mode, a default story that has little control over continuity due to linked threads, or a continuity-minded default story with multiple repeating threads due to no linked threads. Anything else is simply impossible. And to that end, I side with the first one.
Forcing game mode would be a stop gap but I think it would annoy more people than it is worth doing
Why? You were complaining the people weren't turning game mode on in the first place. A default would alleviate this, and the warning page can act as a nice greeting to CHYOA's processes. What exactly would be annoying about it?
and again it would still force writers to double back to the intro to add the flags.
No it doesn't. New variables and flags can be added as the story progresses. Or are you proposing that the problem is the writer didn't set a flag in an old thread that would be critical to a new thread? That the site has to make note of something that no one is telling it to make note of? That the site has to now compensate for pure laziness instead of being a testament to hard work?
Like I said what I am suggesting is something more than just a game mode that is forced on. It is a more subtle version of game mode, maybe even one that readers would not even know is actually running for the reasons i pointed out above.
The bottom line is: it's a game mode. Why develop a second game mode when the first one is doing spectacularly? Why not switch to default and a warning page, which would, in all probability, be a simpler programming choice that achieves the same results you're looking for with far less headaches for writers and programmers alike?