I don't think a single index is enough to tell if one country is more developed than another. I took a quick look at the numbers behind the HDI calculation to try to figure out why the ranking is the way it is. All data was taken from the UNDP website: http://hdr.undp.org/en/composite/HDI
The HDI is based on three sub indices: one for life expectancy, one for quality of education, and one for income. The HDI is the geometric mean of the three indices.
Compared to the Central African Republic, Niger has a higher life expectancy index (0.622 vs 0.506) and higher income index (0.333 vs 0.286) while CAR has a better education index (0.217 vs 0.343). Compared to South Sudan, Niger has a higher life expectancy index (0.622 vs 0.574) but has a lower income index (0.333 vs 0.342) and lower education index (0.217 vs 0.296).
Conflict absolutely does affect HDI since it will lower each of the three indices. However, from looking at the three indices and how they're calculated it's clear that the reason why Niger has the lowest HDI is because students don't stay in school very long. Investing in education would bump them up quite a few spots.
Regarding the list of things stacked against them:
- Them being landlocked is a huge disadvantage, but they can still overcome it. The landlocked European countries benefit from having stable neighbours with quality infrastructure. Unfortunately, Niger would at a minimum require Nigeria to develop before they have a chance.
- Farmers in Niger are able to fight desertification by collecting rain water and using it to help trees survive on their property. The trees prevent soil degradation and improve water retention (https://www.smithsonianmag.com/science-nature/great-green-wall-stop-desertification-not-so-much-180960171/). This land still isn't great for farming, but it's something.
- High fertility rates can come down pretty easily. Ethiopia had a fertility rate above 7 from 1971 to 1995, but it's now close to 4 and dropping. Bangladesh had a fertility rate near 7 in 1970, it's gone down to around 2. Rwanda had a fertility rate above 8 but it's now below 4. etc.
Tl;dr - If they invest in education, take care of the environment, and Nigeria develops then Niger will develop as well.