I know it has to do with time and efficiency, and how ISRs take time away from other processes, but I am unclear why this is. I am always told to keep ISRs very short. I am a bit confused why this is.
Normally, ISRs come into scene when a hardware device needs to interact with the CPU. They send an interrupt signal that makes the CPU to leave whatever it was doing to service the interrupt. That it's what ISR must care about.
Now, this depends on many factors, being the hardware environment and the nature of the interrupt maybe the most relevant ones, but it usually happens that in order to properly service an interrupt, ISRs run with interrupts disabled so they cannot be interrupted. This means that the CPU cannot be shared among other processes while it is running ISR code because the system timer interrupt that is used to run the scheduler (which is the part of the kernel that takes care of making the illusion that the CPU can do several tasks at the same time) won't work.
So, if your ISR takes too much time to perform a certain operation with the device, your system will be affected as a whole, because the percentage of time the CPU is available for the rest of processes will be less than usual. This is much noted on old system with PIO hard disks, which interrupt the CPU for every disk sector they want to transfer to the CPU, and the ISR must do the actual transfer. If there's many disk traffic, you may notice things like your mouse moving jerky (because the interrupt that the mouse device sends to the CPU is not attended)
OSes like Linux allow ISRs to defer time consuming operations with hardware devices to tasklets: sort of kernel threads that can share CPU time with other processes, yet keeping the atomic nature of hardware device operations (the OS ensures that there won't be more than one tasklet function -for the specific tasklet associated to the ISR- running in the system at the same time). The PIO transfer from disk to kernel buffers is an example of such operation.