purchase rights to publish from that link (I have)
Why aren't rats found later in deep dungeons? Why do they always camp in the basement of taverns? Well, because they really are a "training" monster. Vampires offer a glimpse on using them at later levels. They can be a creative opponent, if done correctly.
Because rats are so ubiquitous, we should see them everywhere. Why don't goblins ride trained rats? Paizo gave us "goblin dogs" in Pathfinder. But they're not really rats. Why don't orcs have cages of rats (of all sizes) in their torture chambers? Being restrained on a table with 4 or 5 starving rats climbing on me sounds like true torture. Lizard-men and Yuan-Ti should carry cages of rats around, and randomly grab out one to snack on during conversation. Even orcs, goblins, ogres or trolls may do the same. That type of detail gives a whole new inhuman aspect to a negotiation.
Rats in combat are boring. They are ho-hum compared to fighting green skinned slimy humanoids. They are a little too here, and not enough fantasy. We deal with them as enemies because they are a trope. But, they don't have to be.
Imagine a colony of rats that have developed a rudimentary hive mind. Not just a "rat swarm" but something that uses position and numbers to their advantage. Over the centuries, in Mord Mar, a colony of rats has made holes throughout a well traveled room. They have about 75 rat-holes in the ceiling, walls and floor. All of them are interconnected behind the walls. The hive mind has developed a tactic. When the colony is hungry, they attack from all four walls, pushing the prey to the center of the room. Then rats pour from the ceiling attacking those with "soft skin" (no metal armor) relentlessly. Good luck casting a fireball with 200 rats biting at you, Wizard. When a victim falls, the rats open wide enough to let the others retreat, and feast upon the hapless adventurer.
An evil and powerful fighter was polymorphed into a giant rat some time ago by a goodly wizard. Recognizing the battle lost, he fled and began to form a colony of rats of his own. Maybe the evil fighter marks his rats by biting the left ear. Those rats in the cellar have a hook behind them now. This colony has come to the sewers of the city where the goodly wizard lives, and begun to reek havoc. The rats never stay in one place long, using the sewers to search for a way into the wizard's tower. The mayor asks the party for help removing the rat problem. A mystery for the party to sink their teeth into.