I'm having a similar issue where setting the MTU to 1500 and using a match on 
mac address does not stick. This is on a EC2 T2.Medium instance. Actual 
configuration from a dev server:
network:
  version: 2
  ethernets:
    eth0:
      match:
        macaddress: 12:0f:ae:49:5d:06
      mtu: 1500
      dhcp4: true
      nameservers:
        search: [ devbuilds.vpc, ec2.internal ]

$> cat /var/run/systemd/network/10-netplan-eth0.link
[Match]
MACAddress=12:0f:ae:49:5d:06

[Link]
WakeOnLan=off
MTUBytes=1500

$> cat /var/run/systemd/network/10-netplan-eth0.network
[Match]
MACAddress=12:0f:ae:49:5d:06

[Network]
DHCP=ipv4
Domains=devbuilds.vpc ec2.internal

[DHCP]
UseMTU=true
RouteMetric=100

$> ip link show eth0
2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 9001 qdisc mq state UP mode 
DEFAULT group default qlen 1000
    link/ether 12:0f:ae:49:5d:06 brd ff:ff:ff:ff:ff:ff
# manually set MTU
$> sudo ip link set dev eth0 mtu 1500
$> ip link show eth0
2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc mq state UP mode 
DEFAULT group default qlen 1000
    link/ether 12:0f:ae:49:5d:06 brd ff:ff:ff:ff:ff:ff
$> sudo netplan generate
$> sudo netplan apply
$> ip link show eth0
2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 9001 qdisc mq state UP mode 
DEFAULT group default qlen 1000
    link/ether 12:0f:ae:49:5d:06 brd ff:ff:ff:ff:ff:ff

The last netplan commands could be replaced with a reboot with the same
result.  This configuration seemed to help others, so hopefully i'm
simply missing something or perhaps this is related to EC2?

Attaching output of cloud-init

** Attachment added: "Result of cloud-init collect-logs"
   
https://bugs.launchpad.net/netplan/+bug/1724895/+attachment/5219532/+files/cloud-init-logs-2018-12-05.tgz

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https://bugs.launchpad.net/bugs/1724895

Title:
  MTU not applied on private ethernet interfaces

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