I like your idea of making sea routes worth defending, and therefore forcing the player to build up sea power in the earlier part of the game.
My impression from what Firaxis has said, though, is that the presence of roads & harbours will
automatically make resources available to all cities linked by them - i.e., so that those cities can build units/improvements that require those resources. If you are additionally required to
transport the resources to those cities - which is what your concept of trade boats implies - would this not slow the game down immensely? And if you require specially-built units (trade boats) to transport the resources by sea, shouldn't you logically also require specially-built units to transport them by land - i.e., caravans/freights?
I rather shudder at the thought of having to be constantly building & defending caravans and trade boats, just so I can keep on producing military & naval units to defend my caravans & boats, so that I can keep on producing... you get the picture!
However it would be good if you had to somehow establish a
sea route (like a road on land), which could then be blocked by the enemy, or destroyed (if one of the terminal harbours were destroyed). That would be equivalent to pillaging a road - the line of communication would be broken, and you would
then lose the automatic availability of resources between previously-linked cities.
Just a thought.