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.