It seems to me that computational throughput has improved exponentially, but latency for input tasks etc. has in fact worsened in many cases.

Per TFA IPC has improved by about factor of 5, assuming a 3GHz machine runs BBC micro at equivalent performance of 15GHz

Reality for (SIMD) integer math is probably closer to 1000, floating point... probably 100000.

You're wrong :)

IPCs for 6502 or Z80 (4x "faster" clock but 3-6 cycles per machine cycle) processors were at the count of clock cycles per instruction

Even a measly 386/486 were much faster than that.

Enter the Pentium with the ability to execute 2 instructions in parallel.

IPC count were the big gainers recently as well

It is still only 20-30 fold at max on average. So much more came from many thousand fold clock speed increase, and much wider execution paths.

The perceived performance for an average desktop has been pretty stagnant since, I don't know, at least the mid-nineties.

There was a huge perceived improvement when SSDs first appeared.

Softare expands to fill the CPU available.

AKA Wirth’s Law[1]: “Software is getting slower more rapidly than hardware is becoming faster.”

[1]: https://en.m.wikipedia.org/wiki/Wirth%27s_law

Software is being produced faster though.

Didn't cars also follow that pattern?