Ditto @ Vivi and Krissy, Ace Combat Zero deserves to be mentioned in this thread.
The final battle is a great one on one, but I loved pretty much all the squadron battles. There's some great knowledge and wisdom in that game too. Every squadron boss reveals a bit more of the greater scheme that's brewing behind the scenes, leading up to the climax which makes you think about global issues that exist in our world today. I still feel sympathy for A World With No Boundaries and the goal they want to accomplish. The fact that there is hardly right or wrong in that game makes you 'connect' with the enemy pilots, and eventually shooting them down brings some extra value and emotion along. ACZ is a masterpiece.