A must for proper chroma-keying in Motion is using Primatte’s Keyer (the extended version, not the one bundled in Motion). You will miss very few things compared to AE in terms of interoperability (the quality is amazing).
I just finished a 12-minute shortfilm, 100% green screen, that is being shown in 200+ cinemas in Spain, in front of Bruce Willis’ THE SURROGATES.
We had to do all the comp in Motion (and I’m a Shake/AE user myself) due to coordination, versioning and time constraints.