What is this anime movie from the 90s where the protagonist in a jet fights an enemy mech?
I'm almost certain this is the 1993 OAV Super Dimension Century Orguss 02

Details escape me, but there is indeed a gigantic mecha near the end that the protoagnists needed to stop. The hero was injured and couldn't see, so his friend (the aforementioned blue haired girl) helped him see by linking him to her eyes using tendrils that come out of her head. That's her in the eye-catch below: