The CoG guidelines partly agree with you: “Every ending should be awesome, even if it’s a failure or a tragedy. There should be something dramatic and satisfying about every ending… [And] the player should understand why they got the ending they did. There should be enough clues in the text to show how the story led to that destination: references to past events, allusions to stats, etc.”
In other words, every time you read through a CoG work, you should get a satisfying, complete narrative that emerges from player choice. Combined with CoG’s guidance on choices (make them balanced, so that no single option is consistently inferior, and make the consequences of the player choice clear at the time of choosing), the result should be a story that’s both different and good (i.e. fun to read) on every single playthrough. It can end in failure, but it should be a satisfying failure.
Choice of Rebels may well be the game that had so frustrated you. 
It does allow you to die in lots of places (though not until the back third of the game) and some of those deaths are pretty Hobbesian. Does that break the rule about making failures “satisfying”? I’d say it depends on the reader.
I’m writing about insurgency, and like @Cataphrak, I want to write honestly and forthrightly about a lot of unpleasant and unfair things–the horrors of an unjust regime, the struggle to survive in the wilderness, the anarchy that can make people nostalgic for even an awful order (see future games for that). On a cosmic level, like our own, the world of Rebels is brutal and unfair. It can’t be one that clearly telegraphs every bad outcome, or makes a good outcome easy or without trade-offs. The fact that some of its stories end in pain, disappointment, and frustration (as with, for obvious point of comparison, Game of Thrones) is a feature, not a bug.
It’s unsatisfying, but so in the same sense were (GoT spoilers) Ned Stark’s fate or the Red Wedding–by breaking our sense that we’re in a safe narrative space where we know the rules, it reinforces the story’s overall sense of consequence. And there are books and movies that end that way; my favorite horror movie of the last decade (also about narrative rules and how to break them) ends with everyone dead.
This is, of course, a feature that reasonable people can loathe. Not everyone has a taste for the bitter; of those who do, not everyone wants it in their games. I’ve made other creative choices in Rebels that for some readers will enhance the sense of realism, while for others will be absolutely maddening. The fact that the world has its own vocabulary, for obvious example. And the mechanics of surviving the winter will legitimately seem to some “cluttered with unnecessary realism”.
These are matters of taste, and you can’t write for every taste. I’ve written for my own, knowing it’s not universal. Some people don’t have a taste for bad endings–as witness this thread–and others do, as witness a good number of Choice of Rebels reviews. (Especially on Steam. I guess any community where the Dark Souls series can become a massive hit is ripe for other masochistic art…)