The front end needs more presentation to the user. Specifically deck creation. Sorry to harp on this point but, building decks will be very key to your game outcome. Making it so equipping your crew is easier and you can pick exactly which card is selected.

Something like, you select a crew and it opens up a tree view of all the slots that can be equipped. Then enable the player to drag and drop their cards onto the tree slots. This would greatly assist new players, as there is more visualization of crew and equipment.

Selection of cards could be done via list box kind of selection list. Once a card is selected, if there more than one, a list of the cards shows, enabling the player to select a specific card. It would be nice if the upgrade levels of upgraded items could show as well, as some items are not at the same upgrade level.

Other than that, I was going to suggest Pets!! Extra fun level :)