I agree with much of what you've said, and as a Muse fan from the very beginning, I've also followed with interest the fluctuations between their more introvert material (such as Microcuts, being a good example you've mentioned), to more mainstream offerings like Starlight and TIRO. Personally, there's been little of their material I haven't loved, and I particularly enjoy the way they can switch between tracks have an anthemic quality for sing-alongs at festivals, and their more experimental stuff, that is less-obviously accessible.
I'd class USoE somewhere between the two camps. There are aspects of it that people will recognise and draw comparisons to, the Queen one being the most obvious, and those will lead it to be considered more of a pop song than something like Ruled by Secrecy, say. However it is still a long way off what I'd consider a conventional arrangement, and it's still thoroughly Muse, which for me means a sound that no other band around is capable of imitating.
Lastly, I do know The Black Parade well, but it still doesn't carry any comparison for me. I actually think it's a good pop song, even though I haven't got a lot of time for MCR, but regardless, I see Muse's sound and theirs worlds apart. Anywho, genuinely thanks for taking the trouble to explain your point of view, even if we'll agree to disagree.