I realize that ships cannot yet be upgraded, but assuming an upgrade feature will be added, I'd like to see a non-cash option in addition to the payment options available in GCII.
I think it would make sense to be able to dock a ship at a starport and have an "upgrade" interface that allows players to convert starport production into upgrading a ship. Implementing this would possibly require the starport to temporarily cease working on anything else, so a ship being built would be "paused" until the upgrade is completed, and then normal production would resume. Another option may be to have upgrades leach a portion of normal production and have both normal production and the upgrade happening simultaneously.
I also think this would be a nice option for ship repairs--especially for ships with heavy damage. Instead of orbiting a planet or starbase for a dozen turns to repair, use a starport's production for a turn or two to complete the repairs.