Since I really like both Echo and TSR (Adastra is a whole other can of worms) I'd have to disagree with you. And I say this despite me absolutely getting fucked up by the Echo "good ending is just the less bad ending" sthick.
Those stories were never meant to be happy ones. They were from the start about a horrible place, with horrible people and horrible circumstances. The endings reflecting that is what I honestly prefer over some strange happy ending that doesn't match the story.
But what I think these types of games really need to do is have proper synopsises and tagging. If I as the reader can see from the start that this is not a happy story and will not be a nice or comfortable experience then I can go in with that mindset and enjoy the stories for what they are, instead of expecting something that never was promised.
Go ahead and slap a giant red warning saying "THIS GAME IS NOT A HAPPY GAME, DO NOT EXPECT HAPPY THINGS" everytime you boot up the game if that's what you have to do. Just make it clear that this is not just another slice of life dating VN.