My favorite parts comes from combining of Diffie–Hellman operations on both long term and ephemeral keys to integrate identity verification and creation of deniable shared secret into one operation.
It's a really elegant extension of NaCL's secret box to include Perfect Forward Secrecy.
There are some things that are objectionable.
GPL licensing makes Open Whisper Systems a gate keeper to using the battle tested code base for most users. This is probably unnecessary. It isn't that hard to implement yourself giving a working curve library.
We need to better explain to developers with Ellitic Curve Crypto and Curve25519 aren't scary just because the math is a little unfamiliar and that RSA and integer field Diffie Hellman are code smell.