I had always wanted to use the actual subway system. Maybe even convert a train car to a mobile base without a car. Especially if I was going for an albino-rat guy, navigating the subways of the apocalypse. It would be great way to meet a middle ground. Oh, how about a quick idea structure for what the Cataclysm could one day be?
Sewers = Boat base, minimal carrying capacity or a small enclosure base underground acting as a hub for travel.
Subways = Train Car base, limited to subways only and chance of crashing a blockage, or travel hub base again.
Ground = Car base, uses fuel but offers maximum mobility on the ground, or regular base that will allow for a defensible potion not limited by walls or place on the overmap, including the fact you can just take over pre-existing buildings
Air? = Hot air balloon that allows for MAXIMUM maneuverability with weight limits but invulnerable to zombies (except ranged), or flying airship or tree house for staying out of the way entirely.