I agree with almost all of your points. The story was originally planned for two seasons. At the success of the first season, a decision was made to go with two movies (more lucrative) instead of a second season. As a result, about half of the second season material was cut, resulting in the choppy and disjointed nature of the movies.
Saki just waits for him. Until:
- he shows up (unlikely)
- she settles for Osugi, who really does care for her (more likely)
- she happens to fall in love with someone else (most likely)
I disagree that the feeling was mutual. Although she was swept off her feet by a handsome dashing mysterious figure who came into her life just when she was dissatisfied and looking for a way out, he really is just a friendly guy who loves everybody.
She may have felt it was fate and his deep feelings for her that kept him returning and holding out his hand to her, but really, like a cat, he only showed up when he needed something from her. He would have gone to anybody else if it was more convenient and not given her a second thought.
He is a great man on a great (if nebulous) mission and has no time for anything that would interfere with that mission.