This is a great mod that massively enhances what can be done with rail networks so kudos to the creators but it does have a few little bugs holding it back.

Lane managing
A complex rail network with many lanes going the same direction becomes difficult to manage when trains all prefer to use one particular lane. TM:PE allows use of the lane connector tool however the trains mostly ignore the lane connections and derail to jump between the tracks! Since the 1.7 update this behaviour has become the norm without using the lane tool - The trains behave like road vehicles and jump lanes often. Trains can stop before jumping lanes which can congest the entire train network. examples here.[imgur.com]

Terrain glitches
After placing one way tracks then saving and reloading there can be holes in the terrain or very tall spikes or deep holes. These glitches are typically a few metres wide but can be much larger. Updating the terrain by reshaping it, placing/removing props or trees and painting makes the glitches go away until the next time the save is loaded. examples here.[imgur.com]

If you have any ideas for solutions to these problems or improvements post them here so they don't get lost in the comments.