There's several reasons Apple doesn't have quad cores in their iPhones. They don't do it because they don't need to, and it doesn't make sense for them to. Quad Core isn't inherently better, it's a tradeoff.
#1 is to preserve battery life - Apple, due to the smaller phones use considerably smaller batteries than their competitors. The iPhone 5's 1440 mAh battery is less than half the size of the battery in the new LG G2, and about 55% of the size of the battery (2600mAh) in the Galaxy S4. Still, Apple gets good battery life in their phones, with industry-leading battery life per mAh. It takes smart engineering to achieve that (although obviously a smaller screen size helps cutting down on battery usage too).
#2 is that Apple, in its yearly schedule and fall release time, has focused on improving per-core CPU performance very aggressively. So, while a quad core Krait CPU was dominant early in the year, Apple has improved its Swift CPU architecture to the point that a dual core A7 has very competitive CPU power, especially in non core-intensive applications.
Basically, just like on the PC, there's always an issue of going for a powerful single/dual core CPU vs. less powerful quad core. Yes, power gating/throttling means that on the desktop and even in mobile you can often have your cake and eat it too - the CPU cores shut off when they're not being used, but it still kills battery life when they're all working.
#3 is that Apple puts very powerful GPU's into their phones. The iPhone 4S/5 and now 5S have extremely powerful graphics processors and that takes die space. In order to keep costs down, there's essentially a die size "budget" so everything is a series of compromises to make your SoC competitive but not prohibitively expensive to make. Apple have made the engineering compromise to go for a powerful dual core CPU with a very powerful GPU, rather than a quad core with a less powerful GPU. It was a smart choice to make for the present time.
I fully expect Apple to transition to a quad core CPU at some point in the future - particularly in the ipad, but currently it's not holding Apple back at all.