Fabia has a strong body, good space - you will feel that you are sitting in a big car. Price is high but seating comfort is very good. quality of interiors is also good. Fusion doesn't have the looks & quality of fabia.
Ford service centers are more compared to Skoda. This is more important factor if you are not living in city.
Ford extra warranty scheme is really good. skoda doesn't have one like that. Skoda dealership in Andhra Pradesh is a monopoly - in terms of service, its really bad.
Service charges and spares are very expensive and repair time is also ridiculously long.
Fusion is a value for money as others wrote. Though both these are hatchbacks, the difference is the premium price and premium quality of Skoda.