SPOILER
I think they made a very bold decision, whether people like the ending or not. We've seen games have less-than-happy endings before, but this... man, that's dark as hell. As noted by others, you never actually do get to kill Joseph- you never get that catharsis (or lack thereof, if you take what Jess said to heart), Hope County is in ruins- if not the rest of the country, maybe even the world, if Joseph really did predict the end of the world and not just Hope. It's... really, you lost. As a wise bald man in red pajamas once said, it is possible to play the game exactly right and still lose. That's life. And it really seems to be the case here- no matter how many side quests you finished, no matter how many outposts you liberated, no matter how much damage you did to Eden's Gate, you still lost. Really, so did they- few of them will have survived the bombs, after all. Even Joseph- his family, both real and adopted, are all gone, and the only person he has left in his life- for better or for worse- is the person he rightfully hates more than any other.
I find myself thinking of the original ending to Fallout 3, which fans hated enough that it was eventually semi-retconned in the Broken Steel DLC. Very different situations, but both were grim endings in which the player didn't get to walk away from their choices. But in Fallout, there was still a catharsis- the man who murdered your father and brought untold suffering to the Capital Wasteland, Col. Autumn, could either be threatened into leaving or be killed by your hand, depending on your choices. You faced down the monster, your archenemy, and dealt with him. That Ubisoft made the decision here to not allow you the same here with Joseph Seed before everything goes to hell, is a very bold move, and while I'm not as big of a fan of that ending as I'd have liked I at least salute the decision-making.
(It also makes the decision to do three DLCs that have absolutely nothing to do with the original game premise make some sense- yeah, no further adventures in Hope County after that! I almost wish they did allow you to go back post-credits to see a nuclear hellscape version though, add a few missions to search for survivors, perhaps even recreate the malarial infection from Far Cry 2 as radiation sickness.)
One last thing. The past few games have sold well enough, this one included, that we can almost certainly expect Far Cry 6 in a few years. Small details from 3 found their way into 4, both worked into 5 here and there... one of those being everyone's favorite mentally-slow rocket specialist, Hurk. If no one else survived Far Cry 5, if everyone else is either ash or trapped in a bomb shelter for years to come... Hurk lives or we riot. ;) (And yes, I know there's virtually no way you could actually have him do so without using a whole mine's worth of handwavium, but... come on, it's HURK!)