It's not bad. New Way to be human, Love is the Movement, and Gone I wish were there, but at least they incuded some nice non-singles, especially The Beatiful Letdown, which imo is the best song from that CD. Too bad Sooner or Later and The Blues aren't on there. I'm glad they skipped You Already Take Me There and American Dream, I never got into those. On Fire and Concrete Girl are the only tracks that I question being on there, but they're both pretty decent songs. I do wish they would have used Chem 6A, Might Have Ben Hur or Edge of My Seat instead of Concrete Girl though.
Overall, I like it.
You're basing this on personal preference, which is fine if you're making your own mix. I'm trying to base it on the songs that appeared to actually be Switchfoot's most popular. "Best" is subjective, so I usually take it to mean "greatest hits and fan favorites". Fan favorites tend to show up a lot in live setlists even after the album starts to age. "The Beautiful Letdown" is on neither list, regardless of how much you or I may like it (and it is a good song; there are no bad songs on TBL other than the iffy "Redemption" in my opinion).
NP: "My Deliverer", Chris Tomlin