I've been thinking about this a little bit... It seems like with the change to 10/25 shared lockout, and the difficulty of 10 mans, while most top guilds competing for world firsts are 25 man guilds.. Maybe they can admit that 25 mans are just the top level of raiding in the community?
10 man guilds will always be popular to small groups of friends who don't like dealing with other people, are comfortable in their smaller groups of people, and don't like the idea of having to run 25 mans. In the community, it seems like right now, 10 mans are SEVERELY overtuned to the point of ridiculousness on some fights. Class stacking is impossible, raid composition is more important, and mainly, because 10 man guilds are trying to compete with 25 man guilds that have an infinite amount of additional resources than they do, do to sheer volume of players, characters, utility, everything.
What if Blizzard decided something along the lines of this...
1. 10 man raids are easier than 25 man raids. They tune the fights so 10 mans are not A LOT easier on heroic, but ever so slightly easier than 25 mans.
2. Separate world first/server first achievements and rankings into 10 and 25 man categories again.
3. Keep the system where 10 and 25 man raids drop the same item level loot.
4. Allow 10/25 man raids to remain accessible to most people. Challenging content for most people, but hardcore raiders and top players will most likely not have much trouble downing all regular modes. Heroic mode is for them.
5. Make fights like Ulduar again, where there is a method to "unlock" heroic mode encounters. You have to EARN your heroic mode bosses by performing some task during the encounter. FAVORITE.... SYSTEM.... EVER!!!
6. No more Heroic mode only bosses. It isolates the population when only top guilds can see a certain piece of content during it's tier. Like I said, Regular modes are for people who want a big challenge. Heroic modes are for people who want the ultimate challenge.
Creating two different brackets, one for 10 man heroic mode competition and one for 25 man heroic mode competition would make a lot of sense. 25 man will be seen as the big dog, while extremely slightly less difficult 10 man will be the almost big dog.
With an Ulduar system, it is much more intuitive for hardmodes... Basically, in order to get heroic mode encounters, you have to do something in the encounter that proves you are capable of performing the fight on heroic.
This will also allow them to tune 10 mans for the majority of players, which will give better access to content to everyone. If the encounter isn't challenging enough for you on normal, strive to unlock heroic mode next week!! Everyone wins when heroics are this way, no separate lockout for heroic mode stuff, just prove you have what it takes to unlock heroic, then do your business. If you can't unlock it, do it on normal, get more gear and come back next week.
It's very similar to motocross. There is the MX Lite class and the MX class. MX lite class is smaller bikes (smaller raids), they aren't quite as fast, but they have to tackle the same obstacles as the big dogs. It is slightly less prestigious, but they are competing in the class they are comfortable with, and they still get recognition for their achievements. The MX class is the big dog class, you take on mammoth tasks in heroic mode and earn the spoils that come along with accomplishing those feats.
In short, I think 10 and 25 man guilds competing against each other will always be a flawed system, because they can never truly be equal. It's not feasible mechanic wise, talent pool wise, utility wise. Admitting that they are not equal is the first step to balancing them correctly.