The worst element of sea and river travel is that the relative speed to land travel is compromised- this has always been a major flaw of the Total War series, where armies move as fast as fleets, for example.
The American Civil War might be one of the few settings where navigable rivers are a gaming feature- doesn't AGEOD's version feature navigable rivers? Not strictly a 4x, but then you couldn't have one based on the Civil War anyway.
You may be right to emphasise trade and transportation, however there are a few other aspects you need to consider. Trade was often stifled because it was more convenient for states to tax trade than anything else- as an example, Britain and France continued to trade during the Napoleonic War because Napoleon felt it was lucrative, ironic considering he was supposed to have attacked Russia to stop Russia trading with Britain.
However, as a counter-example, the Spanish were disdainful of trade and were able to dominate Europe almost purely on the basis of plundered treasure from the Americas. It might be true that had they invested in trade and industry at all they might have been powerful for longer, however the Spanish dominance lasted as longer or longer than that of other European countries- and longer than the current American dominance.
One aspect of Sins that I've never liked is the everlasting nature of resources, very counter to real life examples. Also with Sins you cannot capture anything at all, planets are razed as soon as they become neutral. I consider these elements counter-intuitive, and to make for duller gaming.