Because there are a lot of parasites and bad icky things that don't necessarilly get washed out 100% every time. Ever since Seiya and Kalec both got ick when they shared the 10g, I've just been paranoid about certain things. So I'm just taking an extra step of precaution; any bad water with potential diseases in it I dont know about yet goes in the bad bucket, only clean, treated water goes in the good bucket.
It also especially helps to not transfer diseases between tanks a bit, so that not a single drop from a dirty tank touches another tank during changes.
Unfortunately, lol, I am not buying each tank it's own water change kit. So I figured two buckets was a good system to control diseases going down the drain and not into the other tanks. =)