TL;DR
Either in the station or the train schedule have an option to skip stations when destination is full.What ?
One can make trains skip stations that are full by disabling them. But that is a purely binary option: all trains vs. no trains. This doesn't play well with the train station limit. I'm suggesting extending the train station limit feature so trains can skip stations instead of waiting with a destination full message.This could go one of two ways:
1) In the train station have an option for trains to skip the station when the train limit is reached. A negative limit could be used to signal "may skip" allowing this to be activated via circuit network and wouldn't even need any GUI work.
2) In the train schedule add an icon after the station name that can be toggled on or off. The icon would say weather to skip the station when destination full. This would be more work and I'm not sure of it's usefulness over option 1.