of course the main issue is that it shouldn't matter who runs the trains. They should just be 'operated by..' Normal people don't care if it's first capital connect, northern or southeastern. There should be two bands like.. erm.. Regional Railways and InterCity. Those made sense to the public. Ticketing should follow that logic. Valid on InterCity or Regional services (although it will be a challenge to get to that now!)
I'm not sure if I good understand you, but polish railway logic isn't good...
Because, you have Przewozy Regionalne (Regional Transportation) which have train Regio and InterRegio. Regio is old local train. Run in one province and stop on all station. InterRegio run between 2 or more province, and stop not on all station (like a "express train"). This is one company.
Second company is PKP InterCity which have InterCity, Express, Express InterCity and TLK ("cheap railway lines"). All this trains stop only at large stations. And all haven't the same tickets. All have another tickets.
And all going everywhere. Not like a Southeastern and Southern. They have another route. Yes, have common stations, but is only few and ticket on all route you buy only one.
In my city (Zabrze) I have one more company, from 1st October 2011: Koleje Śląskie (Silesian Railways), and is sister-company of Przewozy Regionalne (Regional Transportation), because this and this is managed by marshal (I'm not sure this letter. He's like a "president" of province). And of course, Koleje Śląskie (Silesian Railways) have another tickets and timetable. Timetable isn't on station, where is timetables of Przewozy Regionalne and PKP InterCity in ONE timetable. Koleje Śląskie have timetable on platforms.
And if you going from Zabrze to Warsaw? If you haven't Express to Warsaw, or if you don't want pay so much, you have train from Zabrze to Czestochowa by Koleje Śląskie, and from Czestochowa to Koluszki and from Koluszki to Skierniewice by Przewozy Regionalne, and from Skierniewice to Warsaw by Koleje Mazowiecie (lika a Silesian Railways, but in another province).
And on from point A to point B you going by 4 trains, and buy 3 tickets, because one train (like a Express) is expensive... twice!
Greetings,
T-Karmel