My first connection contribution ;)
To add some more to that: Assuming difficult sites are less visited I checked for each site with less than 2 visitors how difficult it would be to get there. I also took a look at the map and added those sites with nothing nearby... Starting with Africa. I do assume we are not flying around in private jets.
Feasible in < 2 days per trip:
* Air and Ténéré Natural Reserves, Niger: Day drip from Agadez (WHS, 100km). Unsafe.
* Okapi, Congo: Virunga is 250km. Should be feasible in 8h. Probably unsafe.
* KAHUZI-BIEGA NATIONAL PARK: Clustered with Virunga, Okapi, ...
* Socotra (Yemen): Can be done from Sanaa by air plane, so should take less than 5 days.
* Sukur, Nigeria: Can't find any travel tips for this one. Looks like you need to get to Yola and from there you would be able to get there. No sites in proximity. Could take more than a day back and forth. Unsafe.
* Sangha Trinational, Cameroon: Dja Reserve should be two days travel from/to here.
* Dja: You need to get to Yaounde first. From there at least a day's travel. Next site (Sangha) probably also two days away.
* Garamba, Congo: Either from Okapi or from Juba this will probably take more than a day travelling. Also, South Sudan definitely not safe.
* Lakes of OUNIANGA, Tchad. In the middle of the Sahara. No sites at all in the proximity. 4x4 from N'Djamena. Unsafe.
* Salonga, Kongo: Major cities and Okapi both > 50km away. I think 2 days travel time each way is safe to assume.
* Manovo-Gounda St. Floris National Park. No site in proximity. No airport either. 2 days travel effort per direction seems reasonable.
* ALDABRA ATOLL (Seychelles): Pretty clear candidate simply reading Paul's review.
* Vallée de Mai (Seychelles): To get in and out of the place will probably take two days each.