By most accounts, dailies are the number one issue in Mists of Pandaria. Personally, I didn't have an issue with the dailies in Pandaria, mostly because I didn't really care about them and did them desultorily. I'm still not exalted with the Klaxxi, the Serpent Riders, or the Anglers.
I think the issue with dailies was not so much the actual dailies, or even the fact that you had to do dailies to earn reputation. I think the main problem was that Blizzard chose to make reputation the mechanism to deliver alternate raid gear.
I think that link between reputation and raid gear coupled dailies and raiding too tightly together. It would have been better if that link was not as strong. Previous expansions had epics, but it was usually only a single piece per faction.
If I was redoing reputation, here's what I would have done for the expansion launch reputations:
1. i450 blue gear at Honored. i463 blue gear at Revered. Cosmetic items at Exalted.
This moves dailies and reputation down in the chain. Instead of being on par with raiding or high end PvE, reputation is on par with dungeons and scenarios.
2. Items cost gold instead of Valor.
Valor and reputation made for a double gate that was somewhat unnecessary. Simplify things by going back to just gold. Valor could be saved for separated raid gear vendors, upgrading, or simply dropped all together.
3. At Exalted, sell a Bind-On-Account Tabard that allows you gain Rep from dungeons, scenarios, and raids.
This is to help alts out. Your first character has to earn reputation the hard way, but subsequent characters have more options in how they earn reputation, and can earn rep simultaneously with dungeon gearing.
4. When patch 5.2 came out, add i489 epic gear to Exalted on old Reputations.
This keeps the rewards coming for the older reputations, adding additional catchup mechanisms, and adding rewards for the pure solo player.
Essentially, I think that putting reputations on the same level as raiding was a mistake. Reputations would have functioned better one level down, on par with 5-man dungeons and scenarios.