Ghostcrawler has stated in the past that 10-man and 25-man raids are intended to be entirely distinct progression paths. I'd like that clarified slightly--
Are players who clear both 10 and 25-mans intended to have a significant advantage?
The advantages from doing 10-man raids in addition to 25-man raids are split into two broad categories- Hard and Soft rewards. Hard rewards are things additional gear. You'll gain more pieces of gear total from doing both 10 and 25 than from picking one and sticking with it. Since we can't change that without some sort of insane overhaul to the game, the worth of hard rewards has to vary so that getting more isn't a significant advantage. Soft rewards are things like experience with content and a deeper understanding of fights. I don't believe these can ever be extracted completely, but it's a debate whether they're even meaningful. For now I'd like to focus on hard rewards, specifically gear.
The biggest issue, in my opinion, is set bonuses. For most if not all classes, the two and four piece set bonuses on tier 8 are absolutely stunning. As a tanking Death Knight, I consider my 4pc T8 bonus overpowered in the extreme- Or I would if every other 4pc T8 wasn't equally overpowered. That's a good thing. We like saying, "Wow, this is awesome." The problem, however, is that both 10-man and 25-man pieces contribute to the same 4pc bonus. If we assume that getting a 4pc bonus is a huge jump in player strength and we can get pieces from both 10 and 25 man raids it provides significant incentive for people to do both sizes. Going back to the pieces/player/run concept, in 25-man, 5 bosses drop 2 pieces of T8 and in 10-man 5 bosses drop 1 piece of T8. In 25 man, it's .4 pieces/player/raid, in 10-man it's .5 pieces/player/raid. A person doing only 25-mans will get all 4 pieces in roughly 10 weeks. A person doing only 10-mans will get all 4 pieces in roughly 8 weeks. A person doing both will get all 4 pieces in roughly 5 weeks. Emblems of Conquest and Emalon both give additional ways to acquire gear quickly. In the case of Emalon it's simply additional incentive to do both the 10 and 25-man versions of raids. Emblems of Conquest are even more incentive but *only* if you're clearing 10-man hard modes (which is something GC has acknowledged in the past).
A significantly less important issue involves the initial gearing up during the release of a new expansion. Upon the release of Wrath, the difference between 10 and 25 was meaningless. The difference people looked at was attainable gear vs current gear. If I'm using an ilvl 180 blue, I don't care if I'm upping it to an ilvl 213 or an ilvl 226 epic- It's a huge upgrade either way. A 25-man raid clearing Naxxramas could attain roughly 60 pieces of epic loot per run, or 2.4 pieces of loot per player per run. Adding in Malygos and Sartharion you're looking at maybe 2.6 pieces of loot per player per week from 25-man raids. From 10-man raids, you're looking at maybe 35 pieces of epic loot total, or 3.5 pieces of loot per player per run. A player completing both 10 and 25 man raids can get geared up from blues to solid epics twice as fast as a player who is gearing up from one or the other. I mean, that should be pretty obvious to most people- If you raid more, you get geared up faster. There is almost no solution that can prevent this upon the initial release of an expansion. However, this won't be an issue until the next expansion is released, so we can let that rest... for now.
If players are intended to have a significant advantage by clearing both then that's perfectly fine and top-end players will continue to do both for a huge list of reasons. If we're intended to focus deeply on one style of raiding then the incentives for doing the other size of raids needs to be reduced. Removing the ability for both levels of gear to affect one tier-set would be a step in the right direction- Though only a first step, with many more that would have to follow after.