My opinion for the longest time has been that reputations should be account-based.
Reputation rewards are often lower level then what you get out of dungeons. Even with the addition of Valor gear to the pool, they still are mostly side-grades at best and down-grades at worst compared to what you get in LFR. This means physically going for reputation rewards far in the expansion life-cycle ends up being way less attractive. The only reason we did it in WOTLK and Cata was because we were running dungeons anyways, so why not wear the tabard?
By making the reputations account-based, you give the alt player more incentive to do those dailies for the long haul. He could even use some of the exalted gear, like the Klaxxi weapons, as a boost getting them into the newer content faster.
Blizzard says the reason they don't want to do it, is because they still want the character to have definition, but I say bollocks to that. You made pets, mounts, and titles all account-based, and those were more "character defining" then reputations.