It is a battery design issue for sure. But it's not weird that this is an issue that Apple faces and Android doesn't right now. Let me explain:
Consider a case where an iPhone processor has a peak current draw of X amps and the equivalent android phone processor also has a current draw of X amps.
Now we know that the iPhone cell is usually a smaller capacity than the equivalent android phone; lets consider the iPhone cell to be 1.5Ah and the android to be 3.0Ah.
It's fair to assume that both cells in the android phone and iPhone have similar designs inside. Most cells that I open in mobile electronics are coated around ~3mAh/cm2. From this value you can calculate the area of the electrodes from our capacities above [500 and 1,000 cm2 for the iPhone and Android respectively].
Now when that processor hits it's peak load of X amps, it will be distributed over twice the area in the android cell.
*X/1000 A/cm2 for the Android
*X/500 A/cm2 for the iPhone
The higher the current density, the more likely you are to have damaging processes like lithium plating and local heating.
So how do you correct this with cell design?
Apple could stick with the smaller capacity, but instead of coating their electrodes at 3mAh/cm2, they could coat at 1.5. This means the electrode area to produce 1.5Ah would double and make it equivalent to that of the android cell. However, you need to consider that doing this requires more of the current collector that you coat these electrodes on. That current collector takes up extra volume inside the cell. So ultimately, the cell's volumetric energy density will decrease with this change.
I am suggesting that the iphone cells were not properly designed for the current of the processors there were being paired with; especially as the cell ages and impedance raises. I don't think it's a coincidence that this became a larger issue with the iPhone 6S because this is when the processing power really started to take off.
I believe the issue is further exasperated by Apple having poor control over their cell manufacturers. They need to use so many because of the volume they require that they have a large variance in how the cell's impedance growth changes with time. This industry has many trade secrets so communication between cell manufacturer and the customers is notoriously poor.
Samsung likely has better control because they have Samsung SDI producing cells.