I don't care much for Parachutes (besides Don't Panic, Spies, Yellow, Parachutes and Life is for Living), so I'd pretty much leave that as it is. I'd swap High Speed for See You Soon though. Always puzzles me why that's not there...
A Rush of Blood is, again, pretty good in terms of tracklisting. I'd swap Crests of Waves in and A Whisper out though. Also, I'd make The Scientist the closer and just bump everything else up a place.
X&Y is where I'd really change things. For starters, I'd rename it "Twisted Logic" due to it being a much better title imho, plus X&Y (the song) would be gone:
2 White Shadows
3 Speed of Sound
4 Swallowed in the Sea
5 Twisted Logic
6 A Message / Low
7 Fix You
8 What If
10 'Til Kingdom Come
Viva la Vida or Death and All His Friends' tracklisting is pretty perfect in my opinion, but I would still change it up a bit. I'd retitle the album to just "Death and All His Friends" too.
1 Life in Technicolor
2 Cemeteries of London
3 Strawberry Swing
5 Lovers in Japan
6 Viva la Vida
7 Violet Hill
8 The Goldrush
9 Yes / Chinese Sleep Chant (hidden song)
10 Death and All His Friends / The Escapist (hidden song)
With the exception of Lost!, though, I am very happy with this album's ordering.
Mylo Xyloto is a ridiculous title, and I get the idea behind but I think I'd go for something more traditional. The order wouldn't change that much - with this album particularly it's hard to imagine the songs in a drastically different order, but I would make some changes. For example, renaming the album either, "A Hopeful Transmission" or "Major Minus".
1 Mylo Xyloto (hidden song) / Hurts Like Heaven
2 A Hopeful Transmission (hidden song) / Don't Let it Break Your Heart
4 Princess of China
5 Moving to Mars
6 Us Against the World
7 Charlie Brown
8 Up with the Birds
9 Major Minus / Up in Flames (shortened, no drums version)
10 Every Teardrop is a Waterfall
But as a special free download from the website I'd give away PoC acoustic, which would automatically assume the position of track 9 in the album in your iTunes somehow
And that's it.