The problem has been rewarding SKILL versus simply rewarding TIME SPENT.
All systems will require time spent, but the well-designed ones will balance the latter with more of the former.
In PVE, raids take time to organize, learn, and complete; however, it doesn't matter how long you spend in an instance if you never kill any bosses. Thus raids take skill and time. As a reward, they give very good epics.
In rep grinds (also PVE), they take time to accomplish but virtually zero skill (beyond basic farming). Rep grinds are all about time, not skill, and thus give relatively weak rewards.
In the CURRENT PVP system, it takes time to get honor and tokens. If you win (i.e. have skill), you get these faster and thus get rewards faster. However, if you lose, you still get the rewards... just slower. So you can have NO skill and still be rewarded. This is bad. The trouble has been giving good enough rewards to acknowledge the accomplishments of SKILLED PVPers, while not unduly rewarding those who are terrible at the game.
However, BC presents the solution: the Arena. You will still be able to obtain superior (blue) quality items from the old battlegrounds plus Eye of the Storm, however the top quality epics will come from the Arena.
Why does this work? Because to get epics from the Arena you need to win. If you examine the way the ratings will work, yes you can get items just by losing repeatedly... but it will take a very very long time... as in months to even get an item. The arena will require some time to compete in (to play your matches), but less than current PVE raids and far less than the old PVP system. Thus the arena will require high skill and low time; this means Blizzard can give out items that ARE AS GOOD AS RAID EPICS.
Blizzard stated they intend to try and keep the power level between the Arena rewards and the PVE instance rewards equal; they can do that by having the "arena point" system so that to keep up with the PVEers you will need to keep earning points to buy the new items they add. In addition, you can't just stockpile your points in hope of future rewards because there is a cap. Thus Blizzard has designed a system that (hopefully) will allow the item power progression of the most skilled PVE guilds and the most skilled PVP teams to remain (nearly) equal.
TLDR: Blizzard is trying to keep them the same by adding the arena which rewards skill instead of simply time spent a la how PVE works.