It is special because it has magic powers unlike the other Falmers. This type of Falmer is usually seen on higher levels as it can deal a lot of damage.
These Falmer can be found in Dwemer dungeons, like the normal Falmer, but are usually deeper in. They are weaker to the destruction spell "Ice Spike" than to "Fireball". Using Ice Spike, players can keep the Falmer Skulker at bay until you can kill it.