There is three big advantages actually to planetary contol:
1. Energy Capacity: No planet can have more than 150 energy, and its cheaper at times to build generators on unusued planets.
2. Influence control: See Jirca, where 2 wormholes and a stabilizer equals .4% influence gained per turn through decay
3. Build slots: Each structure can only be built once on a planet, which can suck if you want more production of an item.