What you need to do is get over the intuition that a transit network is supposed to be random access and point to point. Its not. Some places are more important and more likely than others. Don't fall for the trap of compulsively filling in lines until there's spaghetti everywhere and everything that could meet at the ends does. Have core structures, basic sorts of routes. Be neither radial nor mesh, but rather federated with ample chances to make transfers. Think of it as a plumbing problem. Your primary people flow is between cheap rent and good jobs. Other people flows exists, but its ok to use smaller pipes on that.