Raid Achievements Are How Encounters Were Intended
The more Heroic Achievement Encounters I do, the more I am convinced that they are how designers originally meant them to be done.
Lets look at Patchwerk. The achievement "Make Quick Werk Of Him" wants you to kill him in less then three min. Without the achievement, you have an incredibly generous six minutes - something that makes him accessible to entry level raiders who may be carrying 1000 DPS players. The achievement, however, is only doable by strong groups with somewhat-optimal setups and a high level of play by all involved - something that is close to how the original encounter was.
The difficulty of the achievement fight feels about right for an entry level raid for a "hardcore" guild. LOKI hasn't gotten Make Quick Werk Of Him, but we also run a little healer (7) /tank (3) heavy for most stuff. If we were to buckle down for it and tailor the raid to the fight (like we use to have to for all progression content), we'd have it down (and soon will, I imagine).
This also ties into the "bring the player, not the class" idea. With just about any setup, I'm confident we could clear a no-achievement Naxx. As I said, we usually run the same number of tanks and healers for everything, making swaps only on a per wing basis, if at all. However, to do optional achievements, we may need to insure we have certain numbers of certain classes. Class stacking exists, its now just not a necessity / barrier to killing bosses.
Lets look at some other Raid Achievements... And They Would All Go Down Together: Removes the option to zerg single horsemen down, which was not possible in the original because of shield walls at 50% and 20%. Just Can't Get Enough: Adds a higher DPS/Healing/Tanking requirement to P1 Saftey Dance: Everyone needs to succeed at the dance. 100 Club: Its like opting for the aura to hit harder.
Really, non-achievement fights are the optional easy mode. You can skip out on a significant potion of the difficulty, still get loot, and still move on to see the next set of trash/boss models. Also, you can kill everything in an instance while gearing up towards an achievement, instead of clearing bosses one two and three, while gearing up for boss four, and not touching five and six.
What's my take on this? I'm pretty happy, though I'd change two things.
Incentive to repeat achievements - If all bosses typically dropped three pieces of loot, and a fourth with the achievement (of perhaps a slightly higher iLevel), I don't think anyone would complain. It's how OS works, and I get the feeling this is how Uludar will function - Blizzard has indicated that all Uludar bosses are going to have "hard modes". As it stands, there is nothing but personal drive to get guilds to keep getting most achievements they have credit for.
Better Guild Rating based on Raid Achievements - WoWProgress rates guilds based on Naxx, Malygos, OS, and OS+Drake Achievements. While this is a step up from WoWJutsu, I think that it some attention / credit does need to be given to other difficult achievements.
I'd also love an ingame PvE "guild achievement" score - just like you have separate personal and team rating for arenas, have separate personal and guild achievement ratings. Give points to a guild where its 20+ of its members have heroic achievements (or 8+ have non-heroic, in another score), and all of a sudden you can tell how good a guild is by looking at their rating.
So there - I now am completely at peace with this new system, and I would suggest that you be too. Don't complain that content is easy, when your opting to take the easy road - and start cranking up your achievement points - it will be an increasingly important score for how others view you.