You could even limit the cities you can draft from to ones that have an overseas trade route.
Yes, that would be cool.

Though it would really leave you in a bind if all they people that you had contact with declared war on you leaving you with absolutely no trade routes and no way to get any. In real life it would be the exact opposite, you then would be more likely to arm the ships as they really have no other use.
But this would be interesting with the Quanative Resource thing.
We would add a Operational Percentage to each Trade Route. If a Trade Route would produce say 100

, then at %100 percent it would produce 100

, %50 it would produce 50

etc. That would all be relative towards the original amount.
If you acquire resources from it (this is were the Quanative Resource come in) at %100 you get the whole # amount of the resource (Whatever it is, say 8 Coal). At %50 you would get 4 Coal etc.
Basically this percentage represents the amount of ships that are currently plying the route.
Now this percentage is what gets pillaged (Not the route itself) and of course the lower the percentage is, the less you/your partner gets.
It will slowly rebuild itself also.
Now this is where the drafting ships comes in. The more you draft, the lower the percentage falls.
And if that route is canceled for some reason (war/embargo etc) and another one to another city is not opened up, you still have those 'ships' that are no longer being used for a few turns. If you draft any ships the will come out of these before they come from any routes.
Note: Trade routes would not start at %100 efficiency.
I'm pretty sure that there is no limit currently on how many Great Generals you can have in a city... but it would probably be a good limitation to add.
I like the idea of Q-ships. Not too keen on merchantmen, at least no need to invent a completely new transport. Maybe just consider the current transport armed.
These armed merchantmen would use the same graphics as there transport representative. So basically they would just be considered armed..
Dom Pedro's Naval Conscription idea is pretty neat, but maybe pro-rate it for like 10 turns of trade and then convert that to say 50% hammers used towards Armed Transports? With the effect being to shut the trade route down completely for say 20 turns (to represent the time for replacement cargo vessels to come online); Or maybe for 10 turns, plus a period of logarithmic growth to represent the trade route regrowing?
Mentioned an idea above..