The ability to give a ship to one's ally should definitely be implemented, perhaps framed as a "lend-lease" type deal. So long as the two parties are allied, the ships would be under the assigned ally's control. The leaser might be down the ships and resources, but it could be quite the stab in the back later on. Might have to have limits though, both in what kinds of ships could be gifted and how many.
Planetary gifting has... well, let me put it this way: Way back when I was playing Medieval: Total War 2, I HATED the region gifting system. The AI would always request you give up territory and always refuse your own demands, even if the AI was on the verge of defeat. A quid pro quo mindset must be impressed upon the AI before they would ever be allowed to make demands or have it demanded from them. It should also be made possible for a player to establish their own territorial claims on planets in a diplomatic sense, a "dibs" system if you will. Obviously it doesn't mean shit until you colonize it outright, but there is still the diplomatic squabbling to consider. I was just playing a game where an Allied AI did settled a world I was just about to send a colony ship to, but going to war just over that would have been seen as a stab in the back, not a logical response to expanding into my sphere of influence. Some diplomatic dialogue and haggling might have defused the situation or lead to a limited war. And that limited war could easily be placed into the game with a sort of mini-"King of the Hill" type game. Whoever holds on to the planet for a set period of time would get the planet and the war would be over right then and there. The war should not go on for the rest of the game just because I felt my ally was overstepping a little.
And the replace ship option would be absolutely fantastic. You could work it out in a menu like so:
1/1 Capital Ship [add] [unassign]
20/20 Light Frigates [add] [unassign]
4/5 Carriers [replace losses] [accept losses] [add] [unassign]
4/20 Missile Frigates [replace losses] [accept losses] [add] [unassign]
You could access this menu in the fleet management section, allowing you to manage your fleet's forces on the fly. The [add] button would apply to an unassigned ship in the gravity well, the [unassign] button has them leave the fleet, the [replace losses] automatically places build orders as resources permit, and the [accept losses] decreases the maximum ship slots in the fleet to whatever is currently there.
Beats the shit out of creating fleets by drag and click, I'll say.