I have a similar problem with the mikrotik CCR1009(vers. 7.11, road warrior connection). When switching to the 7.x version, iPsec L2tp remained slow. There were no such problems with the 6.x versions.
In the office, the connection is 1gb/s, but at home 600Mbps. L2tp ipsec data transfer speed is not higher than 10-12Mbit/s. Download/upload without using L2tp ipsec vpn works fine, with full line speed.
Configuration for the router only “default rules” plus 2 L2tp rules against https://forum.mikrotik.com/download/file.php?id=48815 (port 500,1701,4500)
You should select ciphers appropriate for your cpu.
Go to routerboard specs page, performance.
E.g. 4011 supports many hardware acceleration ciphers for ipsec.
I use 4011 with following:
Ip-ipsec-proposals
There default proposal.
Auth algorithm : sha1
Encr alg: aes-128-cbc
Ip-ipsec-profiles
There default profile
Hash alg: sha1
Prf: auto
Encr alg: aes-128
Dh group: modp1024
Please check the product page for CPU model and IPSec performance specs. Then check the IPsec specs to determine which encryption method should be used at both ends in order to optimize hardware acceleration.