dagov, i think you should always go by distance. if you want to more accurately get a workout for a specific energy system, then you can choose a distance which will more specifically target a given energy system. for your examples…
with the “3 x 300 @90% with full recovery, or should I give them 3 x 45 second run” example, you could choose a distance that would be covered in 45 seconds instead of prescribing a 45 second run, make sense? in this way you specifically choose a distance so an athlete cant slack off, but you also get the proper energy work.
“Another important question is, whenever I do give workouts based on duration, how do you calculate intensity? Is it the same way you would when doing training based on distance?”
the intensity should be measured the same i believe, but mike knows better than me.
“And lastly, if training based off of duration, lets say for example that my 28 second 200m runner is doing repeat runs of 28 seconds (alactic work). Will she conceivably be able (over time) to take that 28 seconds further out (say to 225m, as an example)?”
conceivably yes, but refer to my response to your first example.