Ever since 10 and 25 man raiding were both equally supported in Wrath of the Lich King it's been a struggle to balance these two sizes of raiding groups. In Wrath, the balancing act was accompanied with gear inequity - the smaller size got lesser gear. Many 10 man guilds felt marginalized, and many 25 man guilds would split up to run the 10 mans for additional loot since the two sizes did not share a lockout. We're of course all aware of how that ended up working out - people complained about feeling forced to run raids twice or even four times on certain difficulties, leading to the current system of shared lockouts and the heroic difficulty toggle.
The current system, with 10 and 25 man raids sharing a lockout and gear has endured since Cataclysm, and it's one of the contributing factors to the death of 25 man raiding. Simply put, it's easier to set up and run a 10 man. Each raid size has its own quirks of difficulty (the difficulty in setting up a proper raid comp for 10s and the feeling of added responsibility per player vs. the often grueling mechanical difficulty ramp up for 25's and the sense of having less space to use to avoid more damage) but all things being equal, a 10 man raid is a lot easier to get off of the ground. It does bring its own problems... it's easier to keep a bench going and rotate players in 25's than it can be in 10s - but a lot of players have opted for 10 man. Patch 5.4 threw a wrinkle into this whole balancing act with the introduction of flexible raiding.
And it is this which has me convinced that flex raiding will replace both 10 and 25 man sizes for raids in the expansion to come. Having a flexible raid size with scaling damage will bring its own design challenges, to be sure, but it will also mean that once your guild hits the minimum raid size (currently 10 players) until it hits the maximum, it will never have to sit a player again. And at the maximum size, it will never have to cancel a raid because 22 people showed up instead of 25. It will change raiding, it will change guilds, but it is probably inevitable and necessary change.
Keep in mind that flex raiding in patch 5.4 will not do this. 10 and 25 man raiding will exist as a tier above flex, which will itself be a tier above LFR raiding. But I see this as a means to test the feature, to determine if it works feasibly and see its pitfalls in action. If for some reason flex raiding proves to be wholly unsuitable or ludicrously gamed by the players (perhaps every encounter will reward a specific raid size so that groups are constantly adding and shedding players to hit sweet spots) it will likely be readjusted and redesigned, and it may well be that flex raiding will require a certain number of tanks or healers to be viable per size of group. However, for patch 5.4 at least, flex is an additional option only.
But if it does work, I don't see any reason why you wouldn't just design future raid content around the flex model. It's a consistent system, one that allows a raid to grow or shrink and still survive (tensions that would in previous expansions often spell the doom of a guild) and keep on playing. It means that making the decision on whether or not to invite a player is made with less of an eye towards filling a roster slot and more about meeting your own social needs. It is, in short, a decision that is friendly to a large swath of the player base. It's not particularly balanced around the needs of the small fraction of the base that pushes realm first or world firsts. And it may well destroy those guilds, or pare them down to minimum numbers.
I'm not blind to the idea that this might well end 25 man raiding guilds. However it also might well end 10 man raiding guilds as well. You may no longer see that distinction made, ever. If you can bring everyone, you may just do so. Words like small, medium and large might well take over - you may see groups that maintain a constant roster of 12 to 16 players and occasionally drop down to 10 or swell up to 19, groups that try their hardest to stay as small as possible, massive guilds rotating people through multiple flex raids in a week. I wouldn't mind seeing the top end of flex raiding go back up to 40, in order to let those few groups with a roster big enough to support it bring their full weight to bear on a raid, because the only real reason not to would be to avoid the load on computers and servers. I'm not saying this will happen, but I am saying that it could.
Flex raiding has the potential to completely and utterly rework how we raid and with whom, to change the way we set up and maintain guilds. It could utterly transform the game. It won't do this in 5.4, but when we finally see what lies beyond Mists of Pandaria, I won't at all be surprised if in 2014 I'm writing about the rise of the 15 man guild because of it.