I think they did good work during TKOL. But you could always play "swap the b-sides" with bands and improve their album based on your own preferences. It just doens't jibe with the bands' concept of what that album was.
My ideal TKOL (not in tracklist order):
1. Bloom (Basement arrangement)
2. Little By Little
3. Lotus Flower
4. Codex
5. Give Up the Ghost
6. Separator
7. Supercollider
8. The Butcher
9. Staircase
Leaving Feral, Morning Mr. Magpie, and The Daily Mail as b-sides.
That version of TKOL is a little longer and a lot more consistent, IMO, which were my problems with it. It was a short, slight, uneven work from a band that had been consistently epic for 15 years.
Similarly, I would've left "Morning Bell (reprise)," "Hunting Bears," "Life in a Glass House," and "Pulk/Pull" off of Amnesiac and included Cuttooth, Worrywort, Fog, and Kinetic. But that's just, like, my opinion, man. They wanted to spend "album time" setting some atmosphere and making those statements, and that's their right.