To increase the transport across the borders I suggest the following:

Instead of having about 6 areas (depending of companies) which is owned by one companie the map is divided in several parts. I call these regions here. At the beginning each company select one region. Inside this region the company is allowed to build transport lines between industries/stations in this region. As the region isn't such big as the areas from the first game the company can build transport lines between industries/stations which required crossing the borders. As a restriction the transport line to build are only allowed to cross 1 border. This restriction may be increased later by the "Central"-company/government. It is not nessessary that the new connection must be connected to the old network, so it can be build in any two regions which are neighbours. It is not allowed to build a transport line inside a region other than the home-region to connect to industries/stations inside the region. If two or more companies cross the same border the central-government build a track to connect these regions and the companies must use this tracks at this point. This required a shared tracks patch like http://www.tt-forums.net/viewtopic.php?f=33&t=37455&p=688282#p688282.

All summaries it means:

• Map is split into several regions (magnitude like 40 regions on a 512^2 map, depends on the number of industries and cities, too)
• One home region for each company.
• A company can build transport lines inside his home region as much as he wants.
• A company may cross ONE crossing line to build a transport line between industries which are not in the same region.
• Maybe at some point (depend on the game development) the companies may be allowed to build a transport line which cross several borders.
• If two or more companies cross a border a global track is build which must be used.
• The central-government may be collect taxes from companies who doesn't respect this rules (So yes, this will be a Roleplay game).
• Maybe some basic stuff like no terraform, no vehicles, no airplanes...

Of couse these rules must be improved like "what about industries on other regions but inside station catch area inside the current region"