An idea I had when trying to figure out how to make teleporter entrancesgo in the right place for complex interchanges:
Change current "stations" for non-road modes of transport (i.e. metro, waterbus) to "platforms".
Create a new type of building, a station/interchange.
Make teleporter entrances hand-placeable.
Each new station building can serve a given number of entrances and platforms. Small ones can only have a couple, big interchanges can have multiple platforms of various transport types. Cims will enter from the street, the station building will act, essentially, as a junction of infinitely small size, leading to all platforms and other street exits.
Obviously you will have to put a distance limit in place so that stations can only serve nearby entrances and platforms.
Other things that could be put in place to make it easier/more elegant.
Naming platforms and exits based on the station they are attached to, eg. if I have a station called "Finchley Road," then metro stops attached to it will be called "Finchley Road, Platform 1," "Finchley Road, Platform 2," and street exits will be called "Finchley Road Station, Exit 1" etc.
Setting the coverage circle to centre on *exits* rather than what are currently stations but would be platforms. This makes more sense for both pathfinding and "realism".
This seems fairly simple. Although I am sure introducing an intermediary step in the platform/teleporter chain isn't trivial, it does not seem outside the bounds of the current architecture. Backwards compatibility might be a problem, but perhaps could be fixed by retrofitting old-style stations with a small 1-1 "station" in the code.
Anyway. I know you get loads of these, but there's another long suggestion for some work.