The idea of the single, monolithic criminal organization obviously comes from Fritz Lieber's Fafhrd and the Grey Mouser stories, which featured a thriving and politically powerful Guild of thieves in the alleys and palaces of the great city of Lankhmar. The Guild brooked no competition and drew a tithe of its members loot, presumably to buy political protection offered by the Guild for its members.
While this is a wonderfully inventive idea, it just doesn't seem realistic enough to be enshrined as a condition to be found throughout every city and village in every D&D world. I'm no expert on crime and criminals, but it seems to me that thieves and assassins would be more likely to associate in gangs, mobs, and families, akin to what is portrayed in films like Gangs of New York, The Warriors, The Godfather, and The Sting.
Such gangs would be focused on a particular leader. Depending on their size, they may or may not self-perpetuating after that leader is removed (either killed or imprisoned for his illegal activities). They would not be exclusive to thieves, but would include all sorts of character classes, particularly fighters and assassins but not exclusing magic-users and clerics, in much the same way that gangs of the 1930's would have not only "muscle", but accountants and bootleggers as well.
If you use mountebanks, I would personally set them apart from this element of criminal society and place them in their own sub-culture, one that co-exists at varying degrees of tension with the more violent gangs (a la The Sting).
I find this a much more engaging and dynamic situation to encourage urban adventuring based on underworld activities. Rather than the once-in-a-few-decades attempt to usurp the power of the Thieves Guild by some upstart, cities would see a constant hum of gang violence based both on retribution for previous attacks or slights as well as power struggles to add territory or new criminal enterprises (Marcus the Stirge controls all of the prostitution in the River Quarter, but the Red Kobold Gang from the Foreign Quarter is trying to muscle in on the action, etc.). The regular constabulary (or the PCs!) would then find itself in a much more difficult position as they attempt to solve crimes, as they don't simply have the dualistic option of "Guild or rogue thief" to consider.
Certainly, singular cities such as Greyhawk or Stoink may buck the trend and have well-established "conventional" Thieves Guilds, but the very fact that such a state of affairs is highly unusual would be enough to add to the uniqueness of the places.