My guild recently conducted a number of tests to really narrow down the cause of the painful raid "input" or "ability" lag familiar to most 25s raiders. The results were interesting; it seems to be caused primarily by healing but is influenced by whether or not you're raiding during "peak" hours.
http://us.battle.net/wow/en/forum/topic/9679038602
My hope is Blizzard can dig more into the problem and identify it, but if guilds would help conduct the test themselves as well and add to the data to support/refute the conclusions, it would be great. The more data and discussion, the more likely we are to see some improvement.