The advanced multibeam satellite equipped with phased array antenna and solid state power amplifiers can generate flexible beams, by managing interbeam interference to serve a very large number of users effectively over its coverage area. Onboard processing (OBP) functionality can enhance the flexibility of a large-scale antenna by speeding up computational processes and saving precious radio link spectrum. In this paper, we derive a cross-layer OBP design of switching/routing, beamforming, and user scheduling as taking advantage of fine spatial resolution capability of phased array antenna satellites. We evaluate tradeoff between OBP computational complexity and throughput performance, showing that the additional complexity of an increased number of switch ports and phased array antenna gain patterning is compensated by high throughput gain achieved by mitigating interference. Our analysis shows that throughput gain for the next generation satellite system can be as high as 40, compared with the conventional multiple beam antenna with travelling wave tube amplifiers, and that beamforming is critical for achieving high spectral efficiency in the crowded service area. We then investigate the impacts of onboard switching and phased array antenna beamforming to practical routing protocols, such as open short path first and routing information protocol.