If by "fundamental battery issue" you mean that all phones have this issue or some comparably severe tradeoff, then no, this is
not a fundamental issue. Batteries don't all degrade at the same rate, and even given a specific battery tech, the way it's implemented in the device can have a dramatic impact on the longevity. Temperature, rate of charging, the degree (i.e. voltage) up to which it is charged, the degree (i.e. voltage) at which it is considered empty are all factors that are primarily in the device manufacturers hands.
Even a few percent overprovisioning can extend life expectency by a lot; and aggressive temperature-related charging (and discharging) throttling can trade peak (benchmark) performance and predictable charging speeds for longevity. I bet apple could make a phone with at least double the battery longevity with 1% price, mass, and size increases, and perf and battery life decreases -- if they wanted to. Of course, those factors are easily quantifiable, and battery longevity less so...
So sure: battery degradation is a fundamental issue in the sense that all batteries degrade - but how they do and what tradeoffs the device makes to minimize that are largely up to the manufacturer, and unfortunately also poorly documented, poorly benchmarkable, and I'm not sure how clearly a warranty would apply - so yeah, the it's a factor that manufacturers are bound to skimp on.
(I wouldn't particularly expect apple to be any worse than the rest of the pack, though).