It's interesting to me how valor point upgrades have replaced raid wide player buffs or debuffs to the fights, as we saw in Icecrown Citadel and Dragon Soul respectively. Perhaps it's because valor upgrades can serve a variety of functions beyond just making one raid easier. At any rate, in patch 5.4.8 (undergoing PTR testing right now) we'll see the valor upgrade system get a bump.
But it's not just the valor upgrades that will be changing. Players who spend a lot of time on the Timeless Isle and have a lot of coins they can't do anything will now be able to exchange the coins for Deeds of Valor, which will be a straightforward swap of 3000 timeless coins for 100 valor points. You'll still have your weekly and monthly valor caps to contend with, but now, you can at least do something with all those timeless coins on your currency tab.
Finally, because we'll be able to upgrade our items twice more (up to the 4/4 upgrade level) the special heirloom weapons from Garrosh Hellscream will also be automatically upgraded, gaining an additional 8 ilevels. This is to make sure that players using those heirlooms as their main weapon don't have to abandon them for an item which can be upgraded.
Head to the official site's forums for more details.