One of the problems is that after youve joined an in progress run, for example starting at the 4th boss, when you re-queue for a fresh afterwards you tend to leave once the 3rd is dead as the fourth is already worthless for you - which in turns creates space for other people to then join a partial run. blizz need to find a way to encourage people to stay on and kill the bosses they've already done, and the 45 valor certainly isnt enough. Perhaps having bosses youve already looted always drop a fail bag so there is atleast something to get from killing it again.
As many have already said, it seems the majority of 'raiders' are doing flex now instead of LFR, which is possibly causing a harder time than usual for whoever is left due to the increased percentage of 'newbs'. Right now its difficult to tell wether this is due to a decreased amount of skilled players carrying the others, or purely down to the new tier/content difficulty and not knowing the tacs. I could be wrong but im pretty sure blizz said somewhere that if it turns out to be down to the lower skill level rather than content difficulty, they would considder lowering lfr to serve its purpose for those actually doing it properly, rather than to the level it currently is where raiders are boosting.
In other words, if all the raiders stop doing lfr and focus on flex/normal/hcs, and lfr is left to its intended audience things would be balanced out. but right now we are in the no-mans land because we dont have the data yet to see what is actually going on