PPP is generally accepted as the more flexible modem interface as it is compatible with many modem vendors and is a widely adopted standard. QMI as a protocol is more chipset-specific and tends to provide more optimized throughput, with a more proprietary control structure.
So if performance is paramount for your application, then QMI is the recommendation. If compatibility with many vendors and easy transition if one goes EOL, then PPP is the recommendation. All of these statements assumes the device is using an OS like linux or Windows. If the device uses an RTOS, then raw socket dials may be more appropriate depending on which stacks are available and then every modem has their unique proprietary standards that must be implemented.