You should go with CSI-capable SoMs when possible. As jippie said, parallel interface adds a variety of issues that can result in reduced performance. In addition, some SoMs (iMX6 Quad) have CSI inputs that have the bandwidth to support more than one camera, provided they are multiplexed properly.
Make sure to take a close look at any SoM datasheets before committing to ensure they have the interface you want, as parallel interfaces sometimes get the CSI label and can cause confusion.