Um... you're sure that you meant to post this in the GC3 forum, right?
The diplo AI is very easy to exploit. More so than most 4Xes, in fact. You can sell it vast quantities of resources it just doesn't need, and it'll hand over ladles full of cash. It'll pay you good money for bilateral treaties that you clearly need and it gets no advantage from. You can spend the whole game just paying the AIs to go to war with each other, even if they hate you. If it weren't for the relations watersheds that physically remove certain treaty options from the menus, it would happily ally with you at negative relations (even though there's a value in another file that is apparently meant to stop it from doing so - this seems to have no effect). The AI is so easy to exploit, they added the diplo lockout timers - those would not exist if players hadn't pointed out how hilariously easy it is. Players can (and do) quite easy win the game in <100 turns on top difficulty levels using alliance victories, because manipulating the AI is so easy right now.
The stacking penalty also doesn't really add much micro presently, since the lockout timers prevent you from just doing the same trade over multiple consecutive turns, so you have to prioritize or accept price gouging. While I'd be thrilled to see the timer removed (because it's just an awful band-aid to deal with the diplo AI's weakness, and SD have been entirely open about that fact), it does have some benefits.
If we had a razor-sharp diplo AI that could judge the values properly (of the kind I'm about to argue can be done in the 1.4 thread with Macsen), then sure, we could ditch the stacking penalty because it would evaluate prices effectively by itself. Unfortunately, presently we don't, we can't and it doesn't. The stacking price penalty is the best defense the AI has against exploitation compared to the clunky, restrictive and at times ludicrous lockout timer.