You are only partly right as they created a mod that removes the main connection “feature”.
I never experienced your second point, but this would be really annoying. Probably just as annoying as the electrification of lines (when I electrify lines I often find too late that some of my trains is stuck – maybe just because a little piece of track is not electrified – and then even lose about all the passengers which takes several years to get up to normal again)
You can also add to the annoying points that road over rail passings (impossible to do, impossible to update roads etc.).
In the end I still find the game enjoyable, but after having played it 2-3 times it rapidly loses interest (all maps are kind of the same). I shall try to install some mods…