I would put Management, VM Networks and vSAN on the same dvSwitch with 2x 10Gbit uplinks. Each uplink interface is then connected to a physical switch. Personally, I would even configure the iSCSI traffic on the dvSwitch. But that also depends on your physical switch configuration. Otherwise, if you have an interuption on one of the uplinks, you may have an HA problem in some cases, because in a vSAN setup the HA communication is handled over the vSAN network and not over the management network.
In addition, I would recommend using NIOC and configuring traffic shares so vSAN doesn't suffer when the uplinks are saturated.
You can configure the MTU at (d)vSwitch level and overwrite it at vmkernel level. That is, the (d)vSwitch has an MTU of 9000 configured, the vmkernel port for vMotion and vSAN as well, and for the management vmkernel port you can use 1500. It is important that the endpoints have the same MTU configured. The switches in the middle can also support larger MTU. So a problem with this setup would be if VM 1 has an MTU of 9000 configured and VM 2 (or an external firewall, computer, etc.) only has an MTU of 1500. But if both endpoint devices have an MTU of 1500, it doesn't matter that the physical switches in the middle and the dvSwitch support an MTU of 9000.
Another pitfall is when your jumbo frame communication hits a switch or switchport which is not configured for larger MTU. For example, if a switch in the middle is not configured for jumbo frames and you are using jumbo frames for vSAN or vMotion or iSCSI. In this case, the packets are dropped. So, you must ensure that *all* switchports in the middle that are used for ESXi hosts and storage are configured correctly.
To make it short:
Set the MTU for the (d)vSwitch to 9000, set the MTU for the vSAN and vMotion vmkernel ports to 9000, configure each physical ESXi switchport with a MTU of 9000 and if you like do the same for the iSCSI storage switchports and iSCSI vmkernel ports and vSwitch. Ensure that virtual machines and management vmkernel port is set to 1500 and also the uplinks and other switchports of your physical infrastructure.