you've got that backwards, bigger phones with bigger screens also have longer battery life. The increase in battery capacity by using a larger case is more than the decrease due to the extra screen space which needs to be lit up.
Or put a different way, default Nexus 4 battery was 2100mAh, default Nexus 5 battery was 2300mAh. People were already complaining about battery life on the Nexus 4, so why did they only bump up the battery capacity by so little for the Nexus 5? For comparison, note that a phone known for great battery life, Motorola Droid Razr Maxx, came with a 3300mAh battery and was still a slim phone.
My point is, just because it's the right thing to do to bump up battery life when using a bigger screen, doesn't mean that the manufacturers will go far enough when doing so.