Debated whether to go with a single large hangar opening, but think that was pushing the era's hull engineering capabilities (nothing of that size was seen until the debut of the Enterprise-D, and that had the benefit of an energy-shield to prevent de-pressurization in an emergency). Didn't like the aesthetics of the Excelsior secondary hull, which basically is stretched enormously to accomodate its shuttle-bays. The dual shuttle-bays seemed the best way to go, limiting de-pressurization events, and adding two dedicated hangar doors - each one is roughly thirty percent larger than the original Enterprise setup, and can take aboard larger auxilary spacecraft - which meant the ship could simultaneously launch and recover much like a modern carrier. The design also offered less of a target than Excelsior, and would be less wieldy to maneuver. And it frees up a lot of volume in the central core of the secondary hull for a number of missions, I.E. long-range stores, extra shuttlecraft, or exploration modules.