To me it's:
1) Origin Of Symmetry - you already said everything about it, but I actually like Feeling Good too, I just got bored of it.
2) (but pretty close) Black Holes and Revelations - I can see where the flaws are and I used to agree, but twelve years later I really started to love it, I don't know why. Pop tracks ain't too cringy and the whole thing has some kind of strong imaginary that really helps keeping the songs together.
3) Showbiz - I'm into emotional music, I love raw and heartfelt stuff
4) Absolution - I used to rank it with OOS as their best, but listening back some days ago I really think it doesn't work well as an album. Most of the songs are great, but sounds like a collection of singles and their relative b-sides to me.
5) Drones - Dead Inside weirdly became one of my favorite songs by Muse. I still get back to that one and to The Handler really often. I like some other song to, but in a way that's like "oh, well, it could've got worse I guess". Sounds bad (how could someone possibly think that hiring AC/DC producer in 2014/2015 was a good idea?). Shitty lyrics. But as a whole, it actually works.
6) The 2nd Law - Actually, this and Drones are interchangeable. I remember getting really pumped by Survival when it came out and I hoped the album would've been something along those lines. It wasn't. It has some great moments on it, but it actually got worse in others. The problem is: it's lazy.
7) The Resistance - booooring. Hate the title track so fucking much it ruins my whole listening experience.