I think that the biggest issues are ticketing and journey information. It is almost certainly impossible to properly coordinate timetables between bus and rail - for every bus departure you move so it matches a rail arrival, it will break a connection elsewhere, or make for an unattractive timing at another major point.
On the other hand, there are minimal disadvantages to having proper through-ticketing arrangements, that work in both directions, to allow a single ticket for a journey. In particular, something that means that if your bus to the station is delayed and you miss the train, you can take the next one without any penalty (possibly not with delay-repay compensation), and also that the Ts & Cs are similar. I think this would still be very valuable even if there was no discount on buying the two tickets separately.
Equally, having a single national journey planner database that can allow any public transport journey to be planned as easily as a simple rail journey would make it very much easier to integrate everything together.
Its interesting that there is often talk of closing bus services that run in parrallel with rail services on threads like this. In many cases, the opposite would probably be more sensible, provided that the bus service was protected so that it could not be cancelled or severely cut in the future. Places like the Isle of Wight, Far North Line, Conwy, Looe etc could all have better journey times, better access to town centres and far cheaper operations if run as a bus rather than a train. The inevitable shouts down that this comment will get is probably a good answer to the question the OP first posted - there are lots of rail enthusiasts and bus enthusiasts, but perhaps less public transport enthusiasts!