Rotom is a rather well hidden Pokémon, you are not likely to see it unless you specifically go hunting for it. It is even well hidden within the area that it is located. Below is how to get it:

Hidden towards the exit of Eterna Forest, there is a little path up that goes to the Old Chateau. Once you have the National Dex, Make sure to go there in the evening or at Night. Inside, you'll find many rooms, some of which have creepy ghosts of people as well as many ghost type Pokémon. Once you're inside, make sure to go upstairs
In one of the rooms upstairs, there will be a Television which happens to be turned on. Click A to see it and you should encounter Rotom, if not...then come back later on in the night. Rotom is at Level 15 so you have to be incredibly careful with it.