I've only skimmed the thread, but have we properly defined the difference between the quality of backup players, and their suitability to fit into our system when required?
This is something that the rags under Ferguson, and more recently I'd argue Arsenal have been very successful at. You wouldn't take most squad players at either over the likes of Milner, Dzeko, Lescott, but they can assimilate those players into their system with greater success than we can.
Of course sending out an entire second string side will always cause a drop on quality for any side, but the key is the difference between the very best and the very worst. It's best explained as a series of peaks and troughs. At our very best, with our first 11, our peak is very high, arguably higher than anyone else is capable of. Unfortunately swap out too many of those players, and our troughs are lower (on average) than someone like Arsenal.
Given this dilemma you have two options. Play a system everyone fits into, or play the system you think gets the best out of the best players. I'd argue under Pellegrini so far we've leaned far more towards the latter than the former, which has given us some incredible performances, whilst at the same time creating some fairly shaky ones when the best players don't feature. It's also developed a huge over reliance on Fernandinho.
Sounds pretty bad, but then you have to look at it on a greater time scale than we're used to. Would you rather muddle through the season accomodating everyone into a style we don't want to play, some of whom won't even be here next season? Or do you press on developing the style anyway, knowing the right additions in the transfer window will allow you to really take off the following season? That's also not to say it won't be successful enough this season to win silver wear either, we just have to be a little luckier with injuries than we have been (and no injuries to Fernandinho).
All the above is largely ignoring that three of what should be our better second string are always injured too.
Either way I agree with LC that we're due a few poor results soon. Some players already look like they've lost a fair bit of sharpness and we've got away with it a bit in a few matches. Just have to hope that at this time of year our competition start doing the same. A few draws/losses a piece for Chelsea and Arsenal would be very welcome. Especially as I really want to win that bloody league cup!