Well, obviously this is a very early stage of work (or at least I hope so).
It could be fun if you add the right elements of turn based strategy to it. There are numerous good examples of how to do it and obviously room for some innovative ideas. Look towards Advance Wars, Fire Emblem, Civilization, and maybe even things like Star Control.
Its not confusing for me, but it will eventually need much better documentation obviously.
Your entire graphic system is going to need an overhaul. End of story. Turn based strategy games are notorious for being the most leanient with graphics, but there is no need for the CGA style ships in this day and age.
Game runs fine.
User Interface needs tons of work if you are going to add all the elements a strategy game really needs to make it, luckily most UI for turn based strategy is menu driven, so all you really need is one good menu for any "macro" actions and click based options for any micro actions.