When a ship type is upgraded, you have the option of upgrading all current ships, or none. I'd like the ability to upgrade how every many I choose, because sometimes upgrading all can be too expensive for my current treasury. I'd also like to upgrade ships (once the initial upgrade model has been made) one at a time. (as funds become available)
I'd like an option on the diplomacy screen that allows me to ask a civilization to remove its ships from my territory. In my current game, a civ that I'm not at war with (in fact I have "warm "relations with them) has parked a troop transport just outside one of my planets. Its intentions are obvious, but I don't want to destroy it because I'd be forced into a war.
My 2 cents.