Currently, waterway paths have infinity capacity, which somewhat break game balance.
Another issue is, that sea pathfinder causes lags, in case of large number of ships and large distances between buoys.
As an results, ships number is often limited or even zeroed in case of multiplayer servers.
In my opinion, the problem with ships routes is that they suppose no challenge and they are really boring. If we take away the "infinity capacity", they will be less used than now.
I propose following solution:
[*]ships are reserving its path to nearest buoy/dock, if there is any free slot;
[*]ships are anchored at buoy/dock, if there is no free slots for proceed to the next buoy/dock;
[*]buoys have capacity limited to 4 ships (standing or heading to);
[*]docks have capacity limited to 3 ships (loading/unloading or heading to);
[*]similar to road vehicles, ship would proceed if is waiting too long, to avoid jam deadlock.
You are suggesting to create bottlenecks for players who abuse ship routes.
And if the bottlenecks are really jammed, do as usual.
The idea seems easy to implement, but I don't see a real improvement for gameplay. I think it is a way of forcing players to use the correct amount of ships and less distance between buoys (something you can already do now as your own play style -or forced by an admin-).
In my opinion, above proposal should solve both 'infinity waterway capacity' and 'pathfinder usage' problems (automatically forcing players with huge fleet to keep less buoys distances),
"Infinity waterway capacity" is not really that efficient if you take into account costs and breakdowns. As it has been previously said, a good use of ships and buoys is better than abusing with several ships waiting at the same dock.
Your proposal won't make "pathfinder usage" of ships really better. Using less ships and more buoys will make the problem less detectable, but that is not an improvement over what we already have now.
Directly limiting the capacity-per-tile by restricting the number of ships per tile (as per trains) is probably unfeasible due to pathfinder issues.
In fact it is easily doable. You have plenty of free bits in water-related tiles. You can force the separation of ships, improve pathfinder use, use multi-docked stations... There are so many free bits in the water-related tiles you can even set which tracks and in which directions ships can take (water lanes).