It has been found that Neanderthals had a gene causing them to be content with their surroundings, and humans had a gene that did just the opposite. If humans and Neanderthals interbred, then these unique genes could cancel each other out. As for H. Floresiensis and Denisovans, we don't even know what killed them. Perhaps they just manage their populations better.
I'd like to see a source for this. It seems hard to tell from a gene what an entire species/ culture's world view is.
Part of the problem with this premise is we know that Neandertals and Denisovans, at least, could freely interbreed with Homo Sapiens. So even if you get them to survive humans migrating out of Africa, all these groups mix to some degree so you're not really going to have different species.
After dealing with the late Paleolithic migration of modern humans out of Africa, the biggest issue will be the adoption of Agriculture. if it happened in the Middle East, as IOTL, and modern humans invented it, Neandertals would end up being displaced/hybridized through much of the old world, much as it now looks like half of modern European DNA (at minimum) comes from Middle Eastern farmers.
This. Whoever invents farming (which will be Sapiens, because as far as we know, they are the only hominid mentioned that both has the ability to farm, and the desire to do so having an appetite for vegetables) will have a population boom that will in all likelihood result in some serious interbreeding.
What if Neanderthals had a hostile isolationist view of humans, and this acted as a wall across the middle east, keeping them from the rest of the world.
You act as though Neanderthals will create one single nation state in a pre-civilization era where every hominid ever lived in family-based groups or tribes. Some tribes will hold this view, others won't, and it is impossible to get a confederacy of all Neanderthal peoples, not to mention doing so during
the Ice Age.
What about diseases? Can they be easily spread between the human species. Take a disease only located in humans, like smallpox. Could this disease which ravaged humanity be transferred over into a Neanderthal population and if so, what would be the effects of it.
This might be a good POD. A genetic twist here and there in bacteria is easy enough to pull off realistically, and if this disease reacts especially badly in Homo sapiens, you've just bought the other human species a lot of time.
Part of the issue I would have here is that homo sapiens are way, way smarter than the others. At some point - after technology has progressed to the city-building stage, the other races are going to be somewhat disenfranchised, even if there's no racial bias. If a Neanderthal can't do math, but is very strong, then you've got a labor underclass already. Of course, maybe Neanderthals are just as happy doing the heavy lifting and letting all those puny Homo Sapiens do the thinking that gets them urban luxuries (like running water).
1st, Neanderthals were of an equal intelligence to modern man. There may have been some differences in abstract thinking, but how different is debatable.
2nd, we have never found a Denisovan skull, so we don't even know how intelligent they were.
3rd, Neanderthal would not make ideal slave labor, they'd tire far too quickly. That is one of their main faults as a species and one of the contributing factors to their extinction- they had poor stamina. We can tell this by examining their skeletons. A Sapiens-Neanderthal hybrid people might work out, and it's a pretty dark place to go, but it's possible.
Also Floresiensis developed advanced tools before humans had tools like that.
Again, I'd like to see a source. As far as I've read, Homo floresiensis never developed tools past what Homo erectus was capable of creating.