"You need to call a function called MpTcpSubFlow::StartTracing() within mp-tcp-socket-base.cc. This function automatically plots (at the end of your simulation) all you need on per subflow basis (RTT, CWND, SST, and etc.).
At the moment this can be activated via ns3 attribute system (in your simulation configuration file) with two (boolean) parameters: LargePlotting and ShortPlotting. For example with the following syntax: Config::SetDefault("ns3::MpTcpSocketBase::LargePlotting", BooleanValue(true)). However, this does not work if the flow type is not defined (e.g. whether it is large or short) when they are scheduled.
A quick fix for you to activate this function on every simulation is to remove the if condition in the line 555 of the mp-tcp-socket-base.cc class."