The lack of being able to properly integrate the transit system is apparent as we wait for the Mass Transit DLC to come out in Cities Skylines. Right now you need to build separate stations to facilitate each different mode. This means each of the transit modes operate in a semi independent fashion although limited transfers can happen.
When Mass Transit comes out the multi-modal stations will clean it up and I should be able to get full effectiveness out of the transit modes working together collaboratively.
In the meantime getting the heavy rail system to play ball is working with industry able to get the goods in and out.