I don't mind the rep part...except for how it interacts with the first part you posted, which is retarded. Basically, JP is completely useless. It doesn't just 'feel' useless, it IS useless. Heroics are a joke and anyone who hits 90 can be decked out long before they'd ever spend a single JP that they didn't arleady have saved up. On top of that, you CAN'T spend it anywhere except klaxxives for several weeks of rep grinding, which by the time you unlock the reps you won't want anything.
Even the valor gear sucks, and is only good as a stopgap, but when you need a ton of rep to unlock it you'll get better in most slots just from lfr by then.
It went overboard. JP should be BETTER than heroic gear, and Valor should be equal to LFR at least or normal difficulty raids (like usual) at the rate that you acquire it. I haven't spent a single JP, and I'm using quest items in some slots still. There's just nothing to get.