I'm pretty sure internal water messes up the path-finding as does sea inlets on coasts etc. So what would be good would be a new impassable land type that displayed as water i.e just like the impassable desert tile but watery looking so you could draw lakes on the land. Land units would see it as impassable land and naval units would see it as land.

Might work with coasts too i.e have a rectangular land region with the "water" tile used to make inlets etc, as long as there was some coast that butted onto the actual sea it might work. Regardless of that though it would help with the internal water/lakes.

Then again maybe it has no effect on the path-finding and i am imagining it :)