In a word, IPC, instructions per clock cycle. Even in most, non-pipelined, strictly in-order processor, some operations take more cycles to complete than others: division is almost always much longer than addition, although some processors simply don't divide or multiply so everything can be equal speed.

Adding more, cache and memory interfaces are important too; instructions don't run without data, and while early computers often had synchronous ram as fast as the cpu clock, that's not possible anymore, data that's not in registers takes time to load and store. Super scalar, out of order execution, etc mask some of that, but not all of it.