Quite. The issues will depend on location, but in many areas express routes will run down bypasses which don't have any stops on them, or main roads away from settlements. We can see what is likely to happen by looking at those places with restored railways or services (such as Borders) or where express buses have been introduced already (such as X5 between Bedford and Oxford) and the withering away of stopping bus services. This can have profound effects on the services to those places not served by the railway or express 'railbus'. Sometimes this could be justified for the good of the majority, but other places will result in one commercial catch-all bus service being replaced by two subsidised services.Like you say, this would have to be determined on a case by case basis. If the majority of patronage is local and only heading to places directly served by the route, then it makes sense to keep the existing local service as an all-purpose bus route. If it’s people making onward travel whether via rail or another bus, a limited stop service would be beneficial, but this would come at the expense of those who use the stops that don’t warrant being served by an express route. With most able-bodied passengers walking slightly further to use the faster express route, expect the all-stops service to be drastically reduced or replaced with a taxishare.
Central Government will of course be wary of the additional funding (esp. as doing one will result in a cry for doing it all over the country), and Local Transport Authorities will not have the funding to pick up the pieces left behind.