Bug 1123320

There was a problem of setting MTU from DHCP (bug 1047083), but that is fixed just in -41.git20131003.fc20.

However, in your case, it may only be a configuration issue. Please realize that your first command only modifies a connection profile named p4p1. You need to re-activate it so that the changes take effect. Is the MTU correctly applied when you do nmcli con up p4p1?

Can you check what connection is activated after reboot?
$ nmcli con show active

And list all connections
$ nmcli con show

Can you attach /var/log/messages too?

I just tried it in an up-to-date VM
# nmcli connection show active
nmcli connection show active
NAME  UUID                                  DEVICES  DEFAULT  VPN  MASTER-PATH 
eth0  b3394931-b18b-49ab-b7cd-042d13ee6b53  eth0     yes      no   --          
# nmcli con show
nmcli con show
NAME  UUID                                  TYPE            TIMESTAMP-REAL                
eth0  b3394931-b18b-49ab-b7cd-042d13ee6b53  802-3-ethernet  Tue 11 Nov 2014 11:29:28 AEST 
# nmcli connection modify eth0 802-3-ethernet.MTU 9000
# cat ifcfg-eth0 
TYPE="Ethernet"
BOOTPROTO="dhcp"
DEFROUTE="yes"
IPV4_FAILURE_FATAL="no"
IPV6INIT="yes"
IPV6_AUTOCONF="yes"
IPV6_DEFROUTE="yes"
IPV6_FAILURE_FATAL="no"
NAME="eth0"
UUID="b3394931-b18b-49ab-b7cd-042d13ee6b53"
ONBOOT="yes"
HWADDR=52:54:00:DC:79:AE
MTU=9000
PEERDNS=yes
PEERROUTES=yes
IPV6_PEERDNS=yes
IPV6_PEERROUTES=yes
# nmcli connection up eth0
# ifconfig
eth0: flags=4163<UP,BROADCAST,RUNNING,MULTICAST>  mtu 9000

Also MTU=9000 after a reboot.
The only difference to previous attempt was the 'nmcli connection up eth0' unless some other update fixed it.

This is the expected behavior.

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