Its not bugs. It's how they built the game. If the trigger for the Thieves guild opening quest is loading into the main riften Cell, but you don't have to preform that load any more, it never gets triggered. The game would've had to be designed from the ground up, or it takes a ton of work arounds. It's just really not worth it for an older game, and some of the scripting might be too tied to other things to change at all.