When it came time for Intel to introduce the successor to the Core 2 microarchitecture, they did it with the i7, a high-end desktop chip. Apple doesn't make a high-end desktop. They make small form-factor desktops and they make workstations. It shouldn't surprise anybody that the desktop i7 didn't get picked up by Apple quickly. When the Nehalem-based Xeons were released, Apple was the first to use them, in the Mac Pro. Much later, Apple was able to get the i5 and i7 into only the biggest of the iMacs, which have always (in the Intel era) been MacBook Pros at heart.
Things have been a bit different in the laptop department because of Intel's anti-competitive behavior with respect to graphics chips. First, they refuse to grant NVidia the licenses they need to make chipsets for the mobile Nehalem processors. Then, they refuse to release a mobile i7 that doesn't contain their pathetic integrated graphics that to Apple (who is trying to ensure all their customers can have GPU-accelerated video decoding and OpenCL) is just a big lump of wasted silicon. Thanks to Intel, Apple's laptops need to add an extra graphics chip to their already-crowded motherboards. That's why none of the 13" machines have gotten an i5 yet: they're too small. In order to put an i5 in a MacBook, Apple would have make a major compromise or get really clever during a complete re-design of the internal layout.
Ars tries to partially attribute Apple's continued use of the Core 2 to a lack of engineering resources due to a focus on the iOS devices, but that sounds absurd given Apple's recent financial numbers. I think it can be entirely explained by the differing and conflicting interests of Apple and Intel. They undoubtedly are watching each other's mobile strategies, but that's not necessary to explain what's happening with the desktops.