The solution I found was to make mangle rules that mark packets TO/FROM the FTP server, and add Queue tree at my desired speed or at line speed for those marks.
This works for me. JUST MAKE SURE YOUR FTP SERVERS HAVE MIKROTIK IP AS THERE DEFAULT GATEWAY :) This is important so that you can user original ip on the the FTP server rather then just mikrotik ip.
Scenario:
172.16.0.0/16 are my pppoe client ip pool.
192.168.250.0/24 is FTP server pool. Behind Mikrotik DMZ.
On mikrotik, I created following rules and FTP servers exempted from dynamic queue rate limit and ftp data delivered at LAN speed , all works ok :)
[Mikrotik 5.x ROS Code]
/ip firewall mangle add chain=prerouting src-address=172.16.0.0/16 dst-address=192.168.250.0/24 action=mark-packet new-packet-mark=ftp-up/ip firewall mangle add chain=postrouting dst-address=172.16.0.0/16 src-address=192.168.250.0/24 action=mark-packet new-packet-mark=ftp-down/queue type add name=ftp-exempt kind=sfq/queue tree add name=ftp-up parent=global-in packet-mark=ftp-up queue=ftp-exempt max-limit=100M/queue tree add name=ftp-down parent=global-out packet-mark=ftp-down queue=ftp-exempt max-limit=100M
[Mikrotik 6.x ROS Code]
/ip firewall mangleadd action=mark-packet chain=prerouting dst-address=192.168.250.0/24 new-packet-mark=ftp-up src-address=172.16.0.0/16add action=mark-packet chain=postrouting dst-address=172.16.0.0/16 new-packet-mark=ftp-down src-address=192.168.250.0/24/queue treeadd limit-at=100M max-limit=100M name=ftp-up packet-mark=ftp-up parent=global queue=ftp-exemptadd limit-at=100M max-limit=100M name=ftp-down packet-mark=ftp-down parent=global queue=ftp-exempt
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