Let's take a look at the melee group in a 25 man raid, for example. You have your mandatory Enhancement Shaman and probably an Arms (or Fury) Warrior, since Windfury and Battle Shout are pretty massive buffs. Then you have the option of a Feral Druid. Their damage is buffed by the group, but aren't reliant on Windfury Totem. Regardless, that 5% crit is a pretty big deal.
You're now left with two spots in your five man melee group. Your options are Rogues, Retribution Paladins, and Hunters. If your raid has a Ret Paladin, they must be in this group. Improved Seal of the Crusader is a large raid-wise DPS boost, but to really keep up in personal DPS, the Retribution Paladin must be in the group with that Windfury Totem.
Hunters have their various group buffs and benefit from Grace of Air if your Enhancement Shaman is twisting totems as he should, but their group buffs are either not strong enough to justify being in the 'melee' group, or can also be applied to casters, so they're good candidates for filling in just about anywhere.
If you have a Retribution Paladin, you have one place left in your melee group. This will, most likely, be a Rogue. All four of those other people in the group are there, essentially, to buff that Rogue. They all have synergy together, but that one Rogue is most affected by those four other people. Most raids have more than just one Rogue, but if you're trying to use the Hybrid synergy the best you can, you'll fall into this situation unless you start cutting people.
Let's throw Death Knights into the mix. We don't know how Death Knights will work, but let's make a few assumptions for the sake of discussion. They're a physical DPS class unless tanking, so they will probably benefit from Windfury Totem and the various other buffs the melee hybrids supply. You either get to remove someone from the physical DPS group, or not include a Death Knight as DPS in your raid.
There's also the issue of Shaman. They're very good in raids. Very, very good. Totems are incredible group buffs, each of the three Shaman specs are viable, and Bloodlust/Heroism rocks the house down. It's not uncommon for raids to take 3-5 Shaman to brand new content.
Should this utility and synergy be nerfed? No. No no no. This utility allows Hybrids to bring a lot to the raid game without overshadowing, and replacing, the 'pure' classes. It also gives raiding that feel of everyone working as a unit, which I find to be one of the most fulfilling feelings of 25 man raiding. In no way am I suggesting this sort of utility and synergy be nerfed.
What was mentioned to me, and what I agree with, is that this synergy needs to be expanded, or implemented differently as the game progresses. Rather than group buffs, increase them to raid buffs. Utilize the debuff system more. Step away from the group-wide aura system.
Take Trueshot Aura, for example. 125 Attack Power is not a substantial amount, not compared to Battle Shout. It doesn't scale like an Enhancement Shaman's Unleashed Rage, either. Let's say we expanded this buff to affect the whole raid. It would give that small amount of AP to the physical DPS group, good. It would also give that AP to the stragglers that don't fit the group. The other hunters, maybe a stray Feral Druid, the tanks. There are three, maybe four people it wouldn't have applied to before, where it makes any difference. The same can be applied to Battle Shout, maybe even Leader of the Pack or Totems. This solves the issue of "which of my teammates is most worthwhile," and their buffs wouldn't completely throw balance off. The casters have no need for that AP, and the melee have no need for an Elemental Shaman's Totem of Wrath.
I am sure these changes wouldn't be simple for the Devs, but it would make class balancing a more welcoming endeavor for the raid leaders. Min/maxing on the edge of the game isn't very fun at times, simply because bad raid balance can mean wipes on fights such as Brutallus. Min/maxing is fun for a lot of people (including me) but not when it means excluding people when you don't want to do so, or can't afford to do so.
Using debuffs more is also something that would be welcome, assuming the debuff limit was raised (again). Improved Seal of the Crusader is essentially Leader of the Pack in debuff form with a lesser effect per player, but a larger effect across the raid. One is a debuff that will work outside of your group, the other is limited to the group.
While the Retribution Paladin is unfortunately dependent on Windfury, his largest sources of utility will work for just about everyone. Improved Seal of the Crusader will help the people in Groups 2, 3 and 4 even if he's in Group 5.
Feral Druids often (but not always) find themselves in a 'floater' group with the Hunters. Leader of the Pack is often largely wasted. A Feral Druid in Group 3 is not going to buff the physical DPS in Group 4. Their utility is more targeted than the Retribution Paladin's own, but the nature of Leader of the Pack prevents it from keeping up.
Of course, this all applies to casters as well, though not necessarily to the same extent. How much it affects your Melee, Casters, et cetera, is largely dependent on your group composition, what stage the game is in when you see the new content, the pace your raid moves, all of those things.
By and large, the synergy is very good, but it's also restrictive and almost a little demanding and unforgiving at times. An eradication of group buffs is certainly not the answer, but the amount of them we have currently is quite overwhelming. Expanding the more 'underpowered' buffs to raid-wide buffs would help this quite a bit, I think, and I'd like to see things go this way in Wrath and beyond.