So you're designing a new rail line, which will require bus connections at many points. These bus lines are important. They extend the reach of the rail line, and they are fundamental to how everything fits together as a complete network that anyone can use.
On some parts of the alignment, it appears logical that many bus lines will terminate at a rail station. This means that they will need to lay over -- sit for a while so that drivers can have breaks -- and that takes space. You also want your rail stations to be vibrant urban places, so redevelopment needs are likely to conflict with bus layover needs for urban space, and it's obvious which one will excite politicians and citizens more.
Yet the layover is essential. If it's not there, buses have to drive further to get to other layover locations somewhere beyond the station, and all that time is money out of the operating budget, that comes at the expense of service that customers can actually use.
The critical problem is how to estimate long-term layover needs. At many agencies, operational service planners who spend almost all their time working in a 1-5 year timeframe are suddenly asked how many layover bays they will need for a project that opens ten years from now and needs to function for 50 years after that. Obviously, they have no clue. They have a sense of how the logic of the network tends to cause lines to converge at a station or not, but they can't guess how high demand will be in 40 years, or even what the size and shape of the buses running then will be. (One reason to expect a renaissance of double deckers is simply the intense presure to conserve curb space while maximizing capacity -- a big problem for the double-decker's competitor, the articulated bus.)
So faced with all that uncertainty, all planning staff can do is guess very high about how much space they'll need, which amplifies the conflict with other development -- and also with project construction cost. In the worst case, the estimated layover need conflicts so dramatically with everyone else's needs that they get ignored.
The conflict is totally understandable from everyone's point of view.
Has any agency solved this problem to everyone's satisfaction?
I'm pretty sure the answer is no, but would love to see some inspiring stories about how you've gotten close.