- Room to spread out:
In a 10m with the same size and layout, the raid has lots more room to spread out to avoid splash damage abilities. 25m raids, with more players, have to squeeze in more tightly, or stack more raid healers to handle the damage. An option on balancing this is to reduce the available size of a room (even in as simple a way as putting a deadly moat of doom encircling the playing field on 10) or to increase the radius (or growth rate) of splash effects. It is likely that Blizzard has already implemented things like increasing damage in other areas to balance out the "spread" mechanics in WotLK; as it is, most 10-mans cannot spread out to fill all of the available space, due to the limited range of AoE heals. This one is a relatively easy fix compared to the others.
There are, on the flip side, mechanics that punish having a smaller raid size, notably mechanics such as heroic blood prince: orbs spawning around the room to reach and dps down, flame orbs to physically tag before they annihilate a player, and a penalty to moving, all combined with the need to spread out from shock vortexes. While a larger raid could spread out initially and move very little while still covering those needs, a 10-man needs to reshuffle itself constantly during the fight to make sure orbs are reached and flame orbs are lessened, while the movement can also kill them and they must maintain a certain distance from each other.
There is one big concern with trying to spread out in a ten-man raid: AoE healing. This is the single largest limiting factor in how far a 10-man raid can make use of a room, as the vast majority of "spread out" mechanics also incorporate raid-wide damage. For example, on Putricide, we have to group the raid together to soak green ooze explosions and AoE heal, reshuffling frequently around slime pools and goo, rather than spreading out as wide as there is physical space. Lana'thel must be organized in as close proximity as possible to each other to maximize AoE healing, for sake of survival. With fewer healers and those healers needing to both raid heal and tank heal together, AoE healing does not allow a 10-man to spread out to use all available room space.
- Class abilities available:
10m raids simply have less room to fit in the full variety of class-specific abilities and cooldowns available, including battle resses and types of tank-saving cooldowns. Alternatively, one battle res in 10m brings back a relative 2.5 of the raid in 25m, and though you have more room in the raid for more battle resses, the devs have considered putting a tied cooldown on a raid's battle resses. Blizzard is already working on addressing this in terms of "herolust" (blame Rahana for the term) by granting mages a similar ability, but the simple fact is that some classes are better in certain mechanics than others. For example, heroic marrowgar and heroic sindragosa favor stacking resto druids due to their high mobility: a ten-man raid without a resto druid (or two) will be much harder pressed to get that fight down. Valithria, meanwhile, favors healing classes other than resto druids.
- Impact of a disconnect or death:
1 player down in a 10m is the same as, by numbers, loosing 2.5 players in a 25m. 2 people down? You just lost a whole party in a 25. Did 5 players just jump ship after killing Toravon in your VoA? You can probably still kill Koralon in a 25, but in 10-man, you're out of luck. Did your hunter just take a swim in the pool of poison? Less of a problem on a 25-man than a 10. Did your MT just disconnect and get a defile on them? That will probably wipe either raid size: better hope their character despawns before it gets too big. A healer get bugged out on the teleporter pad (unable to leave the pad) and not notice until the Lich King is engaged? You might be able to get through P3 without them on 10 after they're destroyed by the aoe in the transition, let's hope they don't get a defile in P2. (...yes, all of these have happened to my raid before. Scary, isn't it?)
While many of these things are dependent upon WHO they happen to (loosing one of 2-3 tanks in a 25 man can be just as devastating as in a ten), the overall loss of dps or healing from a death is magnified by the relative raid size in a ten-man.
- Healer/Tank/Raid ratio:
The relative tank/healer/total-raid-size ratio is different for each raid size. Currently, 10s run either a 1/1/5 or 1/1.5/5 ratio (2-3 healers); 25-mans run between a 0.4/1/5 to 0.12/1.4/5 ratio (2-3 tanks, 5-7 healers). Simply put, there are more available healers than tanks in 25-man raid, allowing for more focused tank-healing without the tank's healer having to worry about raid-healing at the same time. 2 healers in a 10-man with two tanks each have a tank to heal AND the rest of the raid, while those same players in a 25 will have the raid-healing job taken over by 3-4 other players, with split attention being granted to also help them with the tanks (hots, bubbles, cooldowns, etc).
Why does this matter? Well, when gear and raid buffs are homogenized in Cataclysm, the tanks should, in most cases, have the same health pool regardless of their raid size. Damage from the boss will have to be balanced with consideration towards how many healers (in terms of HpS) will have their sole attention on the tank... and to some extent, how many raw healers there are in the raid who have tank-saving cooldowns available to help out in emergencies. Otherwise, if it's the same damage to match the same tank stats, then having more healers available to help that tank in the 25-man (or even just having the complete focus of one healer who doesn't have to OT or raid heal as well) will make it seem easier than in the 10-man. Similarly, designing the boss to do more damage in the 25 (to counteract the higher concentration of healers and cooldowns) will make the tank seem squishier than in the 10, and run a higher risk of a tank being one-shot in the 25 when they could've taken the hit in a 10.
There are other ways to counter this, however: the 25 could require more concurrent tanks (be it by adds or damage-sharing links like Lana'thel/Marrowgar), or adds may do more damage in a 25 than in a ten (requiring more attention from the 25-healer and letting the ten do raid heals in conjunction with healing the add tank), or raid damage could be made more avoidable in the ten, freeing up the "raid healing" to allow those healers to focus on their tanks while keeping the raid healers busy in the 25.
- Dualspecs and Raid Flexibility:
Simply put for 10's, there are fights where you want 2 healers, and some where you want 3, and the difference between them is like night and day when it comes to your raid's dps, as compared to a 25's choice of 5 vs 6 healers. Most fights you want 2 tanks; sometimes you want one tank and an extremely durable DPSer (see my sindragosa first kill! go go offspec kitty-bear "tank."). Some fights simply call for a certain class' niche abilities over another, forcing a DPSer and a tank or healer to swap roles with each other.
This impacts not only your recruitment (looking for specific hybrid classes), but also puts much more pressure on dualspecs and cross-spec skill: you need to know how to play your offspec and keep it geared, as each individual hybrid-class player is much more likely to get called upon to swap their specs than they are in a 25man. Some few players in 25s will swap regularly as well, but it is unlikely that most of them will, simply because their specific dualspec class is more likely to be already covered by a mainspec player. Can a 10m instance be balanced to assume that it is packed with dual-spec-savvy players to fit the specific needs of an encounter? Is this fair to pure dps classes, who may be left out of a 10m raid in favor of a hybrid with dualspec due to varying boss mechanics and a wish for raid flexibility, such as ignoring a rogue in favor of the shaman/paladin/kitty/DK/warrior hybrids who could heal or tank in a pinch?
Even with all of these balancing difficulties the developers face (and probably others I haven't yet considered), they seem to believe they can balance the raid difficulties to make them equal. They've had to do so already, with the further wrench of item-levels to consider; in some cases a 10m version is easier (aside gear level) than a 25m, and in others, the 10m has been more difficult (the most obvious of these is OS3D).
Will it always be equal? No. Will they try their best to make it as equal as possible? I certainly believe so. Will 10m sometimes be harder, and will 25m sometimes be harder? Probably; my hope is that in the balancing, they will balance out the relative difficulty across the instance, even if they can't get the specific boss fight exactly the same difficulty.