Available property size is one differentiation between the two suburbs.
Hovea has minimal services (Fuel, Chemist, Post, Supermarket, etc) located in the suburb. But in saying that, access to those facilities is readily available by crossing Great Eastern Highway into Glen Forest, or travelling for about 5 minutes to Mundaring; a much larger economic hub.
Also, dependent on where you live in Hovea, your phone/internet services may not be at the same performance levels as Glen Forest.
Another consideration is the flight path of Aircraft; Hovea is close (not under) the flight path for most West-East-bound flights for most of the year due to the prevailing winds.