So for those interested i finally managed to create a Mikrotik L2TP/IPSec VPN with dual factor authentication.
It involved creating a radius server in linux using freeradius, then setting up freeradius to use MySQL database for user/pass authentication.
Then writing a script that will update the password inside the database to include the Time based OTP (using oathtool) together with the user defined password via
a simple shell script. Its crude but gets the job done since i couldn't find a more "Mikrotik" way of doing it.
If i get some people interested in how i did it, i'll be willing to type up a small howto.
But yes it can be done