The problem isn't specifically Apple's batteries; it's with current Lithium-ion battery chemistry in general. As a whole, we've nearly reached the upper bound of where energy density and consumer safety are at for providing us with a good battery that doesn't easily explode and gives the phone a constant current. The documentary series NOVA had a good episode earlier in the year that showed some possible alternatives to these https://m.youtube.com/watch?v=gxZrQ5yPsLI

Regarding the slowing down of devices, underclocking the CPU allows for both less power and a lower peak voltage to be drawn from the battery and extends the real usable life of the phone. Others would simply not turn on or pass a hardware test by failing to POST. You are right about new software versions being 'encouraged obsolescence'- a company that pushes features to its older phones knowing they may not be able handle these alongside the older essential ones definitely has an interest in you purchasing a new phone. This could easily be fixed by not having the slimmest phone on the market and instead have a thicker and more easily user-replacable battery.