Something which i noticed and seems pretty odd is the fact that when you send a boarding party to an abandoned ally ship the boarding party instantly becomes a crew for that ally and the ship is returned to that ally.

I propose that once a ship is abandoned it can be captured by anyone, including an ally.

If it was.. for crying out loud why ?

This.  It makes sense that if you come accross an allied ship that is now derilect that you would make an attempt to make it operational and return it to your ally in the spirit of friendly cooperation.  Imagine if the klingons found out the federation recrewed a derilict bop and put it into starfleet service.  Political nightmare.  I think the mechanic is fine as is, as annoying as it may be at times.

how about when you assimilate a ship it gains an attribute boost or borg weapons as the borg impliment their own tech on that ship?

If the Romulans wre to send their troops to a derelict allied ship, they would likely keep it. I think they took a Federation world that was previously taken by the Dominion and people were talking about how dificult it would be to get them to give it back. Ships would probably be the same.