Berserk timers are now as brutally overused as untauntability was in Burning Crusade. There are virtually no bosses in Wrath that do not have a berserk timer. Berserk timers are an awkward kludge, and ideally the game shouldn't have them at all.
What's wrong with berserk timers?
First of all, they are "immersion breaking." No matter how much you play the game as a game I think this matters. Boss abilities fit a theme of the boss and demonstrate the power of the creature you are fighting. Calling meteors from the sky, freezing us in ice, summoning minions and good old fashioned breathing fire are all things that powerful creatures do. Suddenly becoming unbeatable if you fight them for exactly six minutes, on the other hand, is really out of the blue.
Second, berserk timers are often put in just for the sake of it. My guild tried to take on 25-player Beasts of Northrend with 14 people, both for gear and to see if we could do it. After a couple hours of trying we finally managed to get to the end of the fight and lost to the 15-minute berserk timer. It is far from clear what purpose that timer is serving other than to stop us from having fun. Fighting 25-player encounters with 14 people is generally not the best way to get loot. Similarly, a Death Knight managed to solo Sartharion, and the greatest difficulty to overcome was that he only had 15 minutes to do it. Sartherion's berserk timer didn't stop us from beating him with 4 people in appropriate gear, so it is serving no purpose but to limit the fun of people doing strange things.
Third, when berserk timers are actually setting the difficulty of the fight, they limit the raid's ability to play through mistakes. This is especially true in 10-player raids. If a fight requires 2 tanks and 3 healers, then losing 1 dps means losing 15-20% of your damage. If the berserk timer is the limiter that is making the fight challenging, then this is an unrecoverable loss, and the moment someone dies you might as well just wipe and start over. Even if someone dies 75% of the way through the fight, if you were only on pace to make the berserk timer by a few seconds, this can be an unrecoverable position. Playing through mistakes and making the best of bad situations is something the game should encourage, not discourage.
Once upon a time, Berserk timers were a good solution to a problem. The problem was that if you brought a tank and 39 healers to an encounter, then you would win for sure1. A time limit on how long you have to win gives dps a place in competitive content. Without them, you eventually die.
Berserk timers do solve that problem, but there are lots of other ways to solve that problem, and very few modern bosses need berserk timers to make dps matter. If the boss summons adds then either you need enough dps to kill the adds before the next ones come, or you need enough dps to kill the boss before there are too many adds to tank. Stacking buffs or debuffs that make the boss more and more dangerous as the fight goes on serve the same purpose as enrage timers, but don't break immersion, and give a little more leeway to play exceptionally and scrape some extra seconds out if you need them. Rotface summons oozes faster and faster as the fight goes on. On Blood Queen you will eventually run out of bite targets and get mind controlled. Heroic Northrend Beasts releases extra bosses on a timer. Heroic Anub'arak only gives you six frost patches to work with, so the third burrow is basically automatically fatal.
I'd like to see them do away with enrage timers entirely. It's totally fine for Firefighter - after all, we hit the big red button - and maybe for certain other circumstances where there is an in game reason that the fight would be a limited time only. But making bosses do 500% more damage after a certain number of minutes is a crutch for encounter designers, is an awkward kludge solution to an old problem, makes no sense within the game world, and rarely makes the game better.
1. I realize this is a bit of an overstatement, many fights would have required more than one tank, and beating fights with nothing but tanks and healers would have taken forever. There was a real concern, though, that encounters could be trivialized by overloading on healers.