Is there any way to increase the skulls added to the game play in Firefight past the first set, as it does in Halo 3: ODST Firefight? Am I missing something, or did Bungie not expect anyone to play past the first set?
You can fully customize the firefight settings if you start your own firefight trough the main menu. Here is a full list of all the possible customisations.
If you mean for the multiplayer firefight, there is no way to affect those properties, expect selecting different gametypes like gruntpocalypse etc.
No, the game is lacking a second layer of skulls.