Trade Routes/Systems being different in each Age makes perfect sense when you think about it, as does Boat and Land based trade routes being different.
Since we now have navigable/major rivers, it is possible to have boat-based trade between more cities than ever, and those routes should be materially different - for one thing, they were the only way to carry Bulk Goods until railroads.
The change in transportation that ushered in Exploration should naturally also change Trade Routes - among other things, open-ocean sailing makes more routes profitable than before, since it should cut down on transit time. I suspect possible length of routes also changes dramatically and possibly even the types of resources/goods whose benefits can be transmitted. After all, in addition to world-wide exploration, the period 1600 - 1800 also saw bulk cotton and wool transported to Factories and proto-factories to be turned into major profits.
Modern Age seems to correspond with Industrial and steam power. That means railroads and powered ships, which should extend all trade routes virtually infinitely in game and also brings in some major changes in how goods are handled: Containerization, Bulk Carriers, 'unit trains' of 100 freight cars all carrying the same product (coal, iron, grain, etc)
This is very exciting, because I can see the same principle being extended to other systems in the game: Religion, Politics, Diplomacy, and Espionage could/should all change the way they work dramatically between Ages.