I loved all of the Scott stuff (NH/Keith and Deb returning/Dan's death), but that's about it personally.
Other than 9x11, and certain parts of 9x08, 9x10 and 9x13, the season was pretty forgettable in my eyes.
Too much stupidity: Brooke's Xavier crap, the Cheller "bromance", Clay's absolute wtf of a storyline (though it gave CQ Logan and made them somewhat bearable so it wasn't a total loss), Julian attempting to re-write history (in the second-to-last episode no less), etc.
A much better final season than season 8 would've been though, for sure.
I pretty much agree with what you've said above. I would give the Scott storyline a 3.8 (points off for no full-family scenes in the entire season...or series for that matter, the lack of anything Scott-related in 9x12, and lackluster scenes in the only episode they were together pre-kidnapping (9x02)). The Dan, Haley and Dan/Haley-related scenes on their own, I'd give a 4.5. Paul and Joy were the actors that carried the season, imo.
The Brooke storyline with X was awful and made her, and Julian at times, look like they didn't have one brain cell between them. The cafe rivalry was juvenile and the attempt to re-write 9 seasons of history in 9x12 was also cringe-worthy. 9x12 ranks as one of my least favorite episodes of the entire series. I'd give the combined Brooke/Julian storylines a 1 if I'm being generous and that's all for the baby in the car scenes and Julian's interactions with Dan. They should have let him leave the Brooke-bubble more often.
Clay's story was bizarre, but the addition of cutie Logan did wonders for the Clay/Quinn relationship and this was the first season I was actually invested (even if just a little bit) in their storyline. I'd give it a 3 overall.
S9 wasn't a bad season at all, but it benefited from the fact that it followed S8, the worst/most boring season in the show's history. It also stands out because it contains one of the series' best episodes in 9x11, a couple of the series' finest acting performances, imo (Joy in 9x08 and Paul in 9x11), and the series finale which, while while too music-heavy, was a mostly nice, nostalgic nod to the history of the show and gave the show the closure it and it's fans deserved.