One thing I know for sure is that the recent Apple processors are derived from the IBM Power processors (G4, G5). Some of them have the Altivec instruction set, which is a Single Instruction Multiple Data instruction set, allowing vector processing faster than with normal operations.
Why are the speeds lower? More complexity in the silicon, or more complexity in the internal traces. However, lower speeds could be higher performance, compare the Pentium 4 2.0 GHz with the Athlon 64 2.0 GHz (this being a 3000+ processor).
The Apple changed their entire processor line when going from the 68040 processors to the Power derived processors (PowerMac, PowerPC, ...). Apple win that change, unlike Intel with their intended move to Itanium

(however the opportunities for success were much bigger on the Apple side).
If I remember correctly, the Intel processors (8086 and later) store number with the least significant bit first. Motorola processors (680x0) stored the most significant bit first, and the POWER processors were capable to operate in either way (to help the transition to the new Power processors on the Mac). The old programs for the Macintosh were run with a software emulation thingy, running slower on the new computers than on the older ones. However, the programs that made the Apple world go round were quickly rewritten, and the new architecture was more capable of higher processor speeds, had faster memory and faster and wider connections between processor and the rest of the system.