The public transit vehicles that go short distance are optimized for short distances. The ones that go long distance are designed differently. This is feasible, because there is no need for a single vehicle to work both short range and long range routes.

Take busses for example:

• The plastic seats in urban busses are less comfortable than the cushioned ones in long range busses - but this design makes them easier to get into and out of, which you will be doing a lot more when the rides are short.
• Urban busses have less seats and more area for standing and walking. This area allows you to get off the bus more quickly (because there is more room to walk) - compared to long distance busses where once the bus stops at the station everyone who want to get off need to form a line (there is not enough room to not form a line). Short distance busses need this to shorten the time the bus stops at each station - a properly that's less needed for long distance routes, making long distance busses opt for more seats so people will not have to stand.
• This standing area also means you can stand up and move toward the doors when the bus approaches your station - which streamlines the process. Long range busses are less comfortable to stand at, so you are expected to seat until the bus stops.
• Long range busses have storage compartments, so that your luggage won't bother the other passengers. Short range busses don't have it, because it'll make the stops take more time, so all that standing area is also useful because people will have their luggage with them (and it'll also be smaller luggage because most passengers aren't going on long trips)