Where are they now?
I believe that the disappearance of the Gargoyles and Mergoyles is a conundrum that one or two researchers from the Durmand Priory are researching. I don’t recall where exactly I saw these NPCs, though.
Skeletons and zombies are replaced by the Risen. This makes sense, because most of the undead seen in Tyria during Guild Wars 1 are minions of the Undead Lich, who was defeated in the end. (In fact, most of them even drop trophy items that refer to Orr – decayed Orr emblems and the like.)
The areas you mention that have Mantids and Mandragora are not actually accessible in Guild Wars 2. The Far Shiverpeaks are much further north than Frostgorge Sound, and the Charr Homelands visited in Guild Wars 1 are currently marked on the map as the “Blood Legion Home” – quite far north from Ascalon.
Finally, Incubi are a subtype of Fleshreavers. These are still in the game, but quite rare.