Why is this an issue? You cannot change from 25 heroic to 10 heroic and back again and the guilds likely to do this will be out of normal modes within the first week anyway.
The problem is, a ten man raid is extremely likely to never see a type of token. I remember waiting 13 weeks for a conqueror token to drop at Cho'gall. Our deathknight only this week replaced his 384 LFR helmet and still has the 384 tier chest while I will be picking up off-set 410 tier the next time it drops.
1 token would be nice for 10 man - but the drops just seem to go in spirts. We went weeks with Vanquishers, to the point that our Rogue and DK had full MS/OS 397's in a flash; last couple weeks (now that I'm tanking on the DK and not healing on the Pally) we've had the Pally, Priest Warlock tokens out the wazoo. Protector tokens have been kind a steady one drop each lock out over time, nothing really bursty. Shields seem to be more of an issue for us. We've seen one tank shield since the patch dropped, one. We've seen one healing shield since the patch dropped and that was in a alt run where I was pally healing with a priest and druid; but in our normal run it's 2 shammys and me - and no shields.
In fact of all the bosses Blackthorn's drops suck the most for us it seems.
There's something about me and shields - I saw the Baleroc shield drop once and I've run FL so much I'm just shy of exalted on three toons.
I fail to see why 25 people rolling* on, say, 3 generic items is worse than anywhere between 3-15 people rolling on each of 3 specific items separately. If your raid group has an even distribution of classes, then any deviation from mean drop rates is a penalty. If you have an uneven distribution**, then you have a small chance of it being an advantage, and a large chance of it being a penalty.
While it's possible that Blizzard has taken this into account with looting rates, and would change things around in the event that a generic system was introduced, looting becomes more homogenous with only a few edge cases. In the case of tier tokens, I would argue this is a good thing.
Further, I find your argument that a few people use loot council, and consequently Blizzard should not make it harder for them a ... curious one. Player invented systems can evolve - and in this case, it wouldn't need to evolve a great deal - while game systems are binary: they are, or they are not. Game systems for all should not be held back*** for the mutable systems of a few players****
*rolling on, being interested in, needing: whatever terminology/loot system you're familiar with
** in Wrath, we typically had 14-16 vanquisher players per 25-man raid, and 5-6 per 10-man raid.
***Granted, this is a matter of opinion, albeit a case of "would you prefer an even rate of tier loot; or, a small chance of a much higher rate of tier loot, with a large chance of a much lower rate?" which is to my mind, a fairly obvious question: I enjoy some element of probability (will I win the roll?), but too much (will I get a chance to make a roll to win?) is frustrating.
****Definitively, the set of all players who use loot council is a subset of the set of all players; and dependent on the above point, such a change is tot he advantage of the set of all players
Official Dragon Wiggler of the Ashen Rose Conspiracy
While I'm not looking for a guaranteed drop from LFR, I do like this system and it giving me something that is specifically useful to me. So if I win, awesome! I got something and it's useful! I don't mind free loot in LFR at all. It's LFR, it's easy, it's mindless, it's me raiding on a free night for fun and I get something out of it that is a piece of gear.