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Pathologic 2 - it's a really stressful game, but I think it'd be perfect for the criteria. The choices matter aspect are intertwined in both how you spend your time (it's limited and you can't be everywhere at once), and in quests (the more traditional choices, like pick A or B or C). Don't want to spoil any more but it's amazing, you don't need to play the original.
Besides it, I've also heard good things from Pathfinder: Wrath of the Righteous, though I haven't played it personally.
I'm going to go a little against the grain and recommend Fuga: Melodies of Steel and its sequel. It's not exactly what you described, but the game is very adept on forcing extremely difficult and impactful choices on you naturally through its gameplay.
Dragon Age, the original first one. Definitely no really happy endings there...
War hospital puts you in charge of a WW1 medical camp trying to allocate limited surgeons, nurses, medical supplies as people come in injured from the front line.
The Walking Dead by Telltale.
[off topic]
Daemon by Daniel Suarez. A persistent computer virus develops a game where the only way to win is to kill off your team mates. The people who show the greatest willingness to backstab are recruited for missions in the real world.