Reputation gear has higher stats than dungeon drops because it is harder (not talking skill here) to acquire. Nothing wrong with that.
Also the moment you unlock Shado-Pan and Celestials you can stop doing Golden Lotus. Anglers are completely optional for gearing just like Loremasters. Tillers are not needed for gearing either.
You just have to prioritize. Do Golden Lotus (until revered) plus Klaxxi. Then after they unlock do Shado-Pan plus Celestials plus Klaxxi. Once you have those high enough for your rewards you can alternate two or three factions each day until you have all at exalted. After that you just do enough each week to get 90 Charmes and Valor Cap.
Which brings us to: Don't try to cap Valor by doing only one activity. Do some dailies. Run some HCs each week (more than one/day is not effective). There are 3 LFR you can choose from. And scenarios. As I wrote in another thread here, with a healthy mix you get to Valor cap rather easy and without repeating the same task over and over.
I would recommend grouping with guildies not only for dailies but for scenarios and HCs too. Prevents brain damage.
There. You don't miss anything and burnout is much less likely to occur.