The main low-medium cost airlines operating between Seville and Berlin are airberlin.com and vueling.com.
Although airberlin.com does operate some direct flights from some Spanish Airports to destinations in Germany, the bulk of its flights are via its large hub at Palma da Mallorca.
Alternatively, one can consider flying via Malaga Airport. However, it takes 2 hours just to get to Malaga Central Station and then at least another 30 minutes to the Airport on the local urban rail service.
Easyjet.com, Germanwings.com and Airberlin.com operate Malaga to Berlin.