I wanted to wait before replying because you hit some some good points, and they are priorities of mine as well. Economy and Navy overhaul is the next major update coming in June.
In terms of military and civilian factories, they will be in that build. You can decide what ratio is used to produce civilian goods (consumed by Pops to produce taxes or population growth) and military goods (consumed to replenish divisions after combat).
Not transport ships but the same class of vessel. They will be called merchants and they will be used to import and export commodities. Commodities are used by factories to produce civilian and military goods.
Morale is something I am considering as part of a future update around the foundations put down in 0.2.0. Not in scope for 2025 but this could change depending on priorities. I want to add it at some point for history purposs, i.e. the French mutinies of 1917 could stop your divisions from attacking.
Naval warfare will revolve around 4 classes of hulls. Battleship, submarine, destroyer and merchant. This game is based on history and as a result, naval combat is not a major part of WW1. Navies are an extension of the economy, your ability to import and export goods. As well as your ability to deny the enemy of commodities for their economy.
Battleships will still be used to initiate/prevent naval invasions. The other 3 classes revolve around economy and the ability to fuel nation's economy.
Capitals will be added but not in the economy update. They will come in September when diplomacy will be reworked. Capitals will be important when it comes to enforcing war goals.
You have a very good eye for the weaknesses in the game, and you communicate them better than most people people, which I appreciate.