I'd rather revert to lake cities (but only on lake shores, not land cities) being able to build sea buildings if they are connected to the sea. Naval powers based on lagunae that are super easy to defend from open sea is nothing unheard of. I hate having to forsake this approach as Venice when I get a lake start, just because I need the sea route increased reach. Besides, foreign naval routes should be able to reach connected lake cities, not sure if they can now. If really there is a balance issue to have a safe haven for a fleet, why not just give combat or movement penalties to ships while on lakes so they can be picked off by attacking ranged land units (unless canals can be made permanent and allow for enemy ships passage when occupied).
Side point, a fort/canal or city that is crossed by a sea route should provide some gold.