Weapon v Junon made a HUGE impact on me when I saw it on my first playthrough, and remains the cinematic I look forward to the most. I also think it's really well integrated into the gameplay. The timing, the editing, is impeccable.
Shademp is right that FFVII's opening scene is absolutely iconic in a way that Weapon v Junon is not, and for me, that puts it almost in a special category of its own, as a cinematic about which it's hard to be objective. I really like your reasoning about the Opening Scene being one cinematic whereas Weapon v Junon is a series - but Weapon v Junon was the first cinematic I thought of when this poll was set up, and I'm not going to second guess myself now.
tl;dr Both awesome choices