Split raiding. A problem which only affects maybe %0.10 of the player base. However, I feel it is an issue which is important to look into. There are countless reasons for why players would not want to take part in raiding at the top level. Crazy hours, doing tons of research on bosses/classes, prioritizing the game over things in real life (in some cases), etc. Hardcore raiding seems to be on a bit of a decline lately. So, I believe that being able to eliminate one of those deterrents (split raids) can, even if just by a little bit, aid in increasing interest in hardcore raiding, so that this part of the game continues to thrive.
Most of the time when threads like this one pop up, people present possible gameplay changes that would discourage guild from doing split run, like personal loot only for Heroic mode or loot lockout across all characters. The problem with these suggestions is that they not only effect the guilds doing the split raids, but also the general player base. We need to first think about the reason split raids are done in the first place. The answer to which is: to gain an edge over the competition. So, this issue is rooted in the competition. Instead of changing the game's rules to fix the competition, change the rules of the competition. How will/can this be done? Well there are a few ways I can think of, but they all involve progression tracking sites like Wowprogress.
Wowprogress has influence over the progression race. We saw this in action in the beginning of Warlords with them disqualifying guilds who abused the BMAH. Now, i'm not calling for the site to disqualify guilds who choose to participate in split raids, but instead, make a separate bracket. This way, if guilds wish to be part of the main race, they won't do split raids. And those who opt to continue to do split raids will be grouped with only those who are also doing split raids. Now the question is: how would you know which guilds are doing split runs and which aren't? Well, one way to track this would be to check loot distribution among the raid (on heroic, of course) to see what percent of the raid is getting loot, and look at the Ilvl of those who are getting loot. If 100% loot is going to ~20% of the raid and those in that 20% are already higher Ilvl than the rest of the raid, you can be fairly sure that gear is being funneled to those specific people. Also, this system could just be in place for the first 2-4 week of progression, since this is just meant for those taking part in the competition.
Anyways, this is just an idea. It obviously isn't perfect; there are probably parts of it that could be tweaked. But, it is a starting point, and I think the more we talk about it, we can build upon our ideas and create a solution.
TL;DR: Make different brackets for those who do split raids and those who don't.