Disclaimer: This post is information as I understand it thus far! There may be some innaccuracies here, and I hope you guys will help me correct it as the true system is better understood.
Blizzard hath both giveth and taketh away this xpac. That is, while it's likely rep grinding will be easier and less tedious in Wrath, there are more distinct reps to be concerned with, and the new badges work in conjunction with rep to get you gear. Simply collecting a mountain of badges won't get you into the good gear anymore. Generally you must have a combination of both badges and rep with a specific faction.
Sounds more complicated so far, right? Well this is where Blizzard giveth. Rather than being locked in to a specific instance or set of instances to grind faction x, you now "champion" a faction and run any instance you feel like to earn rep with them. You champion a faction by wearing their tabbard while running any level 80 instance. If you want rep with The Buggering Brothers, you're not locked to running Buggering Brothers' instances. Run any instance wearing a Buggering Brothers tabbard to gain rep with that faction. Normal and heroic modes will earn you rep all the way to exalted, though naturally you'll gain faction faster in heroic mode.
Again, the one caveat is that you must be in a level 80 instance for this to work. If you throw on the Buggering Brothers' tabbard an run heroic Nexus, no problem. If you throw on the Buggering Brother's tabbard and run normal Nexus (lvl 72 - 74) you gain no rep.
All factions have mountains of dailys that can be done as well. The quests may change as your rep level increases, but quests will be available all the way to exalted.