I can't speak for whether removal of the brookies is needed (i.e., does the number present threaten native cutthroat populations?), but I can tell you electrofishing is not an effective way to remove fish from a watershed if you need to remove them all. It just never gets them all (and you only have to miss two to have not solved your problem). I've helped with a number of electrofishing surveys related to native cutthroat restoration in Rocky Mountain National Park. These were population surveys--we were just trying to find out how many fish of what species were present. We always make 2 passes through a stretch of stream. What we catch in pass 1 is temporarily removed and held in fish baskets. There are usually fewer fish caught on the 2d pass, but not necessarily a lot fewer. For purposes of estimating the population, the biologist puts the data in a spreadsheet that applies a statistical model to estimate how many fish are actually present.

They could conceivably reduce and control the brookie population with an ongoing electrofishing effort. But why not--I suspect they reason--solve the problem once and for all and after a few years have a self-sustaining native fish population not threatened by invasive brook trout? Their draft CE says they have been electrofishing for 2 decades in an attempt to control the brook trout population, but it has continued to expand. Notwithstanding your observations that you have never seen them doing so and that there are few brookies relative to the cutthroat population, I suggest you seek out their actual data in support of your comments to the draft CE.

And in theory, at least, the rotenone can be applied with minimal effect downstream. They don't have to wait for it to dissipate. They have a neutralizing agent they can introduce at the bottom of the target stretch that stops the carnage downstream. Having said that, there have apparently been failures, including the disastrous 1962 poisoning of the Green River recounted by Anders Halverson in his book, An Entirely Synthetic Fish.