How different they could be would depend on the environment they evolved in.
Here's what you would need to achieve this.
Isolated populations that still have plenty of room to evolve. Take a good look at animals in Australia and the Galapagos Islands. There are animals there which you can't find anywhere else, but the humans, they travelled there about 50,000 years ago, likely by sea from Asia. So, what you want are lots of places that are even more isolated than that--bigger oceans that are more difficult to cross, or hazards lasting 10s of thousands of years which divide land, giving each area an opportunity to evolve intelligent life-forms.
When they do meet, they have to cooperate rather than destroy each other, and they have to be genetically distant enough not to interbreed. Neandertals ended up "disappearing" into modern humans. They were different enough to be genetically distinct, but not so different that they couldn't be absorbed into the population. And yes, many think that they were a different species of the same Genus, Homo, which had a common ancestor.
Cooperation will be more likely if they aren't competing for the same resources and if they each have something the other needs. What that could be is up to you.
How different they would be...well...it's your world and that's WIDE open.