I mean, really though, Visser Three throughout 99% of the series (excluding Hork-Bajir Chronicles and arguably Andalite Chronicles to an extent) was a bumbling mustache-twirling caricature. If he were actually DANGEROUS, to the extent that he believably should be (with that rank, and all the crazy war experience he's had), Jake and the Scooby Gang would have been crushed by about book 3.
I mean, look at Esplin in H-B Chronicles. He's a ruthless interesting ambitious winner. By book #1 he's like that four-armed robot general guy in the last Star Wars movie. "Ha-HAH! I'll kill you alllll, lowly scum! Bwahaha!"
All I'm saying is the Yeerk Pool flushing isn't really worth complaining about. It's just the same as how a naive farm-kid in Star Wars can beat 5 elite military deathsquad guys in a shootout. Dumb, but necessary for the plot.