The main difference is the battery technology and the discharge curve. The Cortex NiMH batteries might have had 3000mAh, but you never use the full capacity for a host of reasons. Voltage sag both due to discharge and load limits you to <20% of the nominal capacity of the NiMH cells (with charge state <80%, your consistency is gone and you risk the Cortex reset under load).
The V5 battery has flatter discharge curve and much better load handling (think of “jumpstarting a car” load), limiting the voltage variations under low charge and/or high load. Also, with smart motors, you could rely on much better consistency accross different charge states, allowing you to run with less-than-full batteries with no worries.