Which MSC Sub Class is the best for USB 3.0?
The USB Mass Storage Class with Bulk-Only Transport was a necessity of USB 2.0 link layer limitations, stemmed from the half-duplex nature of USB 2.0 transfers and lack of individualized responses within transactions. So the EHCI controller had to wait for response before issuing some other sense request. This resulted in sub-optimal bus utilization and loss of performance.

With advent of USB 3.0 full-duplex physical layer, the responses to individual requests/pipes can come back asynchronously, which opened the possibility for implementation of full-scale SCSI interface.

Therefore, to answer the question literally, the best implementation of MSC in USB 3.0 environment is UASP. This has nothing to do with eMMC or any other types of your local storage. However, you must work hard to implement the multi-threaded device-side controller to comply with UASP intricacies and get all performance advantages.

Regarding the support of UASP on host side, this is purely a matter of having the corresponding OS driver, since the whole UASP is purely software thing on host side.