Well, there already is an upcoming R-rated animated movie. Once studios see this is something they can get away with (earn higher profits), we might see more of those coming; perhaps even HTTYD.
However, that's highly unlikely since the franchise has already been established as "family friendly".
But that doesn't mean it can't get dark.
I think killing off the entire Berk is not a good idea though (Hiccup and Toothless being the only survivors is cliché by the way; maybe if a handful of people survived, or were crippled for life, that would make it a tad more bearable as a plot twist, but still not a good idea I think). A lot of people complain about how DWA focuses on the human stories instead of the dragon ones, and I can't say it's not true. But you certainly don't want to suppress either of those too much. The world is complex, and it should be portrayed in all its complexity. Therefore, I want to see a bit from everything. A bit from Toothless' story, a bit of Hiccup struggling with being a chief, a bit of the dragon lore that's behind the behaviour of certain species of dragons, a bit of Hiccstrid, something that would explain how in the world the gang dragons (Stormfly and co.) were so easily tamed at the end of the first movie, a bit from Valka's story, Drago's story, and perhaps a little bit from the every day of live on Berk, how the human and dragon worlds coexist in the same environment, and how Berk fits into the wider picture with other tribes, what are Berk's relations with those. All those details we often overlook in our own lives, I want to see them.
This all is possible in a PG film, but I'm not sure if one can fit all that into 90 minutes when you count the actual story.
Destroying Berk would also destroy a lot of potential they were building during the first two movies. The potential that comes from the events of especially the second movie; will Berkians trust Hiccup as a chief? He barely grew up, Stoick didn't manage to raise him into that role. He's inexperienced, naive (also shown in the second movie), and clearly doesn't want to lead the entire tribe either. His heart is elsewhere. He can't be even half of the chief Stoick was, he simply doesn't have the qualities to be a good leader. What if other houses (for example the Jorgensens) try to use this very rare opportunity and usurp the leadership? I don't see Berk as an utopistic fairytale, humans are simply humans just like dragons are simply dragons. You can't help their nature.
If they make Hiccup the "best chief ever", that's something I'm most likely be not going to be okay with.
Either way, I can totally see Hiccup going rampage after his naive view of the world collapes once the reality starts to kick in. It's easy to lose sanity in such situation, and he might do some very, very silly and bad things. Another reason why he won't be a good chief. Not yet anyway. That would be an interesting twist, and a bit of a revolution too - that there are no heroes and villains, that everyone, humans and dragons alike, have their angels and also demons hidden inside.
One interesting twist would be Toothless becoming a brutal militaristic dictator in his dragon world. 'cause look, he meets all the criteria: rare, secretive, intelligent, powerful, intimidating, something that the hunted fear, and something those who hunt want to get at all costs. The ultimate trophy. Possibly the most bullied dragon species? I think Toothless realizes that he's a member of a very rare species, and given by natural instincts he'd do everything to preserve his kind. Even if it means being a jerk to everyone else. I'd be interesting to see how Hiccup deals with that. You know, power corrupts. Once you get a taste of leadership, you'll start to want more, and more, and more... Both Hiccup and Toothless will be exposed to that temptation. They have to be; otherwise that would be another minus point in my book. But yeah, that's just me being very, very finicky.
I could write like that all day, but I gotta save something for the next post.
One thing is certain, the last movie will be dark to a certain extent. Falling from the golden age of dragons to the moment where they're simply gone in a single human lifespan, that
will have to happen in a rather radical way.
We'll see what the future holds!