I found a mod that nearly perfectly alters the Companions to where you have to meet certain level/skill/quest requirements in order to advance to the next level in the main story arch. It can be found here: http://skyrim.nexusmods.com/mods/22650

Are there any such mods for the Thieves guild or Mage's College? I like the TG jobs, but everything with the main quest seems so..."hurried."

The author of the aforementioned mod has no intentions of doing the same thing for the other two guilds, which is a shame.