I'm running into this issue as well. By moving my "mtu 9000" to the same "post-up ifconfig $IFACE mtu 9000" that I was using for all of my other interfaces, it at least started to actually bring the interface up, and set the gateway correctly. But it is still not setting the mtu properly for the vlan4 device, and only the vlan4 device.

(Irrelevant data trimmed from pastes below)

$ cat /etc/network/interfaces
# The primary network interface
auto enp3s0f0
iface enp3s0f0 inet manual
        bond-master bond0
        post-up ifconfig $IFACE mtu 9000

auto enp3s0f1
iface enp3s0f1 inet manual
        bond-master bond0
        post-up ifconfig $IFACE mtu 9000

auto bond0
iface bond0 inet manual
        bond-slaves enp3s0f0 enp3s0f1
        post-up ifconfig $IFACE mtu 9000

auto mesh0
iface mesh0 inet manual
        bridge_ports bond0
        bridge_stp off
        bridge_fd 0
        post-up ifconfig $IFACE mtu 9000

auto vlan4
iface vlan4 inet static
        address 10.42.0.6
        netmask 255.255.255.0
        gateway 10.42.0.1
        post-up ifconfig $IFACE mtu 9000
        vlan-raw-device mesh0

$ systemctl status networking
● networking.service - Raise network interfaces
   Loaded: loaded (/lib/systemd/system/networking.service; enabled; vendor preset: enabled)
  Drop-In: /run/systemd/generator/networking.service.d
           └─50-insserv.conf-$network.conf
   Active: failed (Result: exit-code) since Do 2016-05-19 07:22:30 UTC; 9min ago
     Docs: man:interfaces(5)
  Process: 3610 ExecStart=/sbin/ifup -a --read-environment (code=exited, status=1/FAILURE)
  Process: 3341 ExecStartPre=/bin/sh -c [ "$CONFIGURE_INTERFACES" != "no" ] && [ -n "$(ifquery --read-environment --list --exclude=lo)" ] && udevadm settle (code=exited, status=0/SUCCESS)
 Main PID: 3610 (code=exited, status=1/FAILURE)

Mai 19 07:22:27 gloss.orion.snow.mesh ifup[3610]: /sbin/ifup: waiting for lock on /run/network/ifstate.enp3s0f0
Mai 19 07:22:29 gloss.orion.snow.mesh ifup[3610]: /sbin/ifup: waiting for lock on /run/network/ifstate.enp3s0f1
Mai 19 07:22:29 gloss.orion.snow.mesh ifup[3610]: Waiting for mesh0 to get ready (MAXWAIT is 2 seconds).
Mai 19 07:22:30 gloss.orion.snow.mesh ifup[3610]: Set name-type for VLAN subsystem. Should be visible in /proc/net/vlan/config
Mai 19 07:22:30 gloss.orion.snow.mesh ifup[3610]: RTNETLINK answers: File exists
Mai 19 07:22:30 gloss.orion.snow.mesh ifup[3610]: Failed to bring up vlan4.
Mai 19 07:22:30 gloss.orion.snow.mesh systemd[1]: networking.service: Main process exited, code=exited, status=1/FAILURE
Mai 19 07:22:30 gloss.orion.snow.mesh systemd[1]: Failed to start Raise network interfaces.
Mai 19 07:22:30 gloss.orion.snow.mesh systemd[1]: networking.service: Unit entered failed state.
Mai 19 07:22:30 gloss.orion.snow.mesh systemd[1]: networking.service: Failed with result 'exit-code'.

$ /sbin/ifconfig
bond0     Link encap:Ethernet  HWaddr 00:25:90:14:cb:d8
          inet6 addr: fe80::225:90ff:fe14:cbd8/64 Scope:Link
          UP BROADCAST RUNNING MASTER MULTICAST  MTU:9000  Metric:1
          RX packets:27794 errors:0 dropped:0 overruns:0 frame:0
          TX packets:78498 errors:0 dropped:4 overruns:0 carrier:0
          collisions:0 txqueuelen:1000

enp3s0f0  Link encap:Ethernet  HWaddr 00:25:90:14:cb:d8
          UP BROADCAST RUNNING SLAVE MULTICAST  MTU:9000  Metric:1
          RX packets:9964 errors:0 dropped:0 overruns:0 frame:0
          TX packets:39249 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000

enp3s0f1  Link encap:Ethernet  HWaddr 00:25:90:14:cb:d8
          UP BROADCAST RUNNING SLAVE MULTICAST  MTU:9000  Metric:1
          RX packets:17830 errors:0 dropped:0 overruns:0 frame:0
          TX packets:39249 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000

mesh0     Link encap:Ethernet  HWaddr 00:25:90:14:cb:d8
          inet6 addr: fe80::225:90ff:fe14:cbd8/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:9000  Metric:1
          RX packets:103632 errors:0 dropped:0 overruns:0 frame:0
          TX packets:7722 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000

vlan4     Link encap:Ethernet  HWaddr 16:4d:22:46:c5:54
          inet addr:10.42.0.6  Bcast:10.42.0.255  Mask:255.255.255.0
          inet6 addr: fe80::144d:22ff:fe46:c554/64 Scope:Link
          UP BROADCAST RUNNING MULTICAST  MTU:1500  Metric:1
          RX packets:14949 errors:0 dropped:0 overruns:0 frame:0
          TX packets:7714 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000

But at least now, I'll be stuck wondering why my transfer speeds are capped at 2Gb/s now instead of “why can I talk to everything BUT the actual server itself?” (I can even access the two virtual machines underneath!)