main advantage of cia files if lets just say tomorrow a update comes out and sky3ds is blocked, so no eshop access for updates etc, and gateway emunand is blocked so no eshop either......with the 3ds you dont need to be on the latest FW to play online, your game only needs to be running the latest patch from eshop(where applicable)....so in this theoretical situation gateway and sky3ds are now stuck on 9.4(emunand)/9.4 and smash bros or pokemon or whatever gets a new patch, with gateway you could still install it and still play online even on 9.4, where as with sky3ds its update and loose the card, or not update and loose online
plus with gateway you get easy region free, rom editing, save editing and all that good stuff