1) Smaller circuits (used to?) have less capacitance and smaller voltages. Smaller voltages and capacitance enables higher clock-rate with same power consumption (chips don't melt)
2) Spending more transistors for pipelines and multiple execution units in the same core speeds up the processing. Single instruction takes at least five clock cycles from start to finish. With pipelines it's possible to finish one instruction per cycle. With multiple execution units it's possible to finish more than one instruction per cycle. This all from a single core.
3) Cache. Lots of it, different levels. Accessing external memory is very slow. Main cache reference takes about 1 ns. Main DDR MEMORY reference takes 100 ns. Waiting for 100 ns. wastes cycles. Adding prefetching etc. is yet another chunk of transistors.
Modern CPUs can execute several instructions per clock cycle doing things like this.
Add a ton of transistors to intelligently prefetch and cache will in some cases decrease those 225 CLKs.
A great deal of transistors are added to cache and cache intelligence to get around the terrible latency of DRAM.
There are more ways to speed up your CPU, like identifying instructions that can be executed independently and issue them in parallel, use caches to speed up loading, etc.
[1] http://www.slideshare.net/dragonpradeep/carry-look-ahead-add...
[1] https://en.wikipedia.org/wiki/Carry-lookahead_adder [2] https://en.wikipedia.org/wiki/Binary_multiplier
The difficulty is in getting all the features you want within the space provided while adhering to the laws of physics.