His one glaring weakness didn't wind up working because Stan and Ford ended up acting retarded, so Bill had to be retarded by not being able to tell the older twins apart. They also had to give him a new weakness he didn't have before where he needed permission to look through a person's memories. He didn't need that from Stan in his first episode. I guess Ford's metal plate is a Deus ex Machina.
Then a lot of other weird things. Why would erasing a person's memories hurt Bill really? A body can die with Bill in it and Bill won't be hurt, but temporary amnesia somehow kills Bill even when the person gets all their memories back a few minutes later? And so on. Of course with the backwards message if they ever wanted to use Bill again if the comics ever get made, he'll turn out to not be dead after all, but there are a bunch of silly and stupid things that had to happen for him to lose.
But it was a comedy show for kids so no big deal. Harping on it is autism which is what /co/ is. It's just one of the problems with making an "all powerful" villain without from the very beginning putting in checks and balances or making it the kind of story where PL don't matter.