Almost every single piece of media, let alone RPGs or the Final Fantasy series has moments where bad stuff happens, otherwise there wouldn't be much of a plot. Almost every story at its base is about the main characters overcoming the hardships and earning a better future.
If you take a nihilist approach to the game, then all you see is the bad things. Literally the whole point of the Scions is a group of people who are waaaaay too cheerful, noble, positive, and optimistic about the world and even after a large number were killed, they move on instead of losing themselves to grief like they would in a lot of other media. They rebuild themselves, beat the bad guys, and continue on to keep being good for no reward. Their attitude is so sickeningly sweet and stereotypical for a group of protagonists that it takes me out of it sometimes.
I don't see FFXIV as a "grimdark" series like Witcher, Berserk, A Song of Ice and Fire, etc. where it's a long series of bad things happening to everyone for almost no reason except to beat the audience with terrible events happening to people to the point where they become numb. The difference is that FFXIV doesn't dwell on those bad things and the characters overcome it with a stereotypical "shounen" gung-ho-ness. At the end of the day in every X.0 and X.3 patch, the heroes of FFXIV, battered and bruised, always come out smiling to celebrating NPCs and acknowledge those who died in the events leading up to it but then turn it onto having hopes for the future. All of it to the fanfare of the Final Fantasy main theme as credits roll.
The whole theme of the game is retroactively very obvious even when you go back to the ending of 2.0.
Merlwyb:
No victory, however sweet, can wash away our bitter sorrows. No triumph can reclaim those we lost. Yet do not presume you honor them by dwelling on the past. It was not the past they fought for. You would repay their sacrifice by looking to the future.
All of the remaining Shards as well as the Source would end. I think that counts as the end of their worlds, unless you are an Ancient who has already been sacrificed to Zodiark or a Convocation member, all of whom are already dead. The whole reason Rejoinings are bad is "returning life to those who have already passed, in exchange for those who are currently living across many worlds", which contradicts what I believe the theme of the game is about.
How do you think Hythlodeus would react if he found out that his friends spent 12000 years killing millions of people just to bring him and the others back when they already sacrificed themselves? Not for Amaurot, but for the Star. Elpis hammers in how much they care about the Star and the cycle of life in general. To bring them back is a slap in the face of their sacrifice. Do you think they did it with the full expectation they would be brought back to life and everything would be hunky-dory like none of that ever happened?