I say the Wraith is better, and no, this isn't because I am a Sangheili fan. The logic is simple really. Whilst a Scorpion beats the Wraith head on, what if the Wraith was around a rock. The Wraith can shoot of the rock with its plasma mortar, hitting the Scorpion before it even gets there.
A Scorpion's shell doesn't bend or curve over, it goes straight. In comparison, the Wraith's mortar curves and dips down, hitting accuracy; distance and height. The Wraith can remain hidden and in cover whilst shooting, whereas a Scorpion can't, it will hit a wall.
Wraith's are also easier to kill hijackers where Scorpions are literally impossible unless you are near a wall. Also, the Scorpion cannot boost to quickly evade damage or hijackers which makes in vulnerable to more jacks and susceptible to more damage. However, the Wraith can use its boost to evade this.
These reasons for me, are why the Wraith is better than the Scorpion.