However, Blizzard also tied the Justice and Valor point gear to the factions. This means that the Group PvE players also have to work on faction reputation to unlock gear.
In Cataclysm, this worked fine because of the tabard system. With tabards, a Group PvE player gained faction reputation by doing Group PvE. So faction rep was gained in doing what the Group PvE player was going to do anyways.
However, in Mists, Blizzard did away with the tabard system. This meant that the Group PvE players now had to do the Solo PvE game in order to unlock their rewards. Naturally, this made them upset, and Blizzard has had to weaken the repuation system, to make it easier, in order to compensate.
I think the major problem was "crossing the streams". The Group PvE endgame content should have stayed separate from the Solo PvE endgame content. To be honest, almost every time crossover happens, be it from PvE to PvE or Solo to Group, there is unhappiness.
And yet, if the factions have gear as rewards, they will be seen as necessary to the Group PvE player. But if they don't have gear, the Solo PvE players don't get to improve their characters by playing their endgame.
My solution would be to offer all Justice/Valor gear from a regular vendor, just like in past expansions. But if you get the faction reputation, you can buy that same gear at a significant discount, say half-price.
So this sets up two paths. If you don't want to dailies at all, you can just run dungeons, get Valor at a faster rate as well as boss drops, and buy gear from the regular vendors. If you do dailies, you get Valor at a slower rate, but eventually you unlock and can purchase gear for a significant discount.
If you do a mix, then you can get some gear cheap, and some gear at full price. You can do the factions you care about, and ignore the others. If you like min-maxing, figuring out the optimal mix of dailies and dungeons would be an interesting exercise.
But essentially, it would make reputation and dailies optional for the players who don't like doing them, since you can always replace dailies with more dungeon runs.