While I believe that Rustboro and Lilycove could make decent capitals due to the size and population of them, I actually think that Mauville might be the best choice to be Hoenn's capital city. It's the closest city to the center of the region, which would make it an easier access point from all sides (rather than someone from say Littleroot or Petalburg trying to get to Lilycove). It also has a bit of an economy going in the games with both Rydel's bike shop and the Game Corner.
The only other option I can think of is Ever Grande City, as the Pokemon League area would make sense as controlling the region. Contradicting it's name though, it isn't much of a city, and with it being located away from the majority of the region on an island, I don't think it would be the smartest location for a capital.