In terms of shortcomings of the series as a whole, I think the film version of Harry/Ginny suffered a lot due to running-time issues. It's not an amazing story in the book either, but I liked it fine; however, the films barely have room for Ginny even when she's plot-relevant (ie, Chamber of Secrets), and it's not helped by the fact that there are two other much more plot-relevant female characters (Hermione and Luna) who share a lot more screentime with Harry and are played by actresses who have much more chemistry with Daniel Radcliffe (Bonnie Wright does fine with what she's given, mind you).
I was thinking much the same thing last night while the Missus and I were re-watching Part 1. I've always thought that Emma and Daniel had much better chemistry together than Em and Rupert or Dan and Bonnie. Even reading the books early on, I thought that Rowling should've steered the two characters together at the end.
But as a writer, I fully respect that it's J.K.'s world and her characters and her decision to steer them as she sees fit. It is a shame though that the films didn't allow for more time to make the Harry/Ginny relationship work better. I'm judging by your comments that Luna played a fairly important role in Part 2 (it's been awhile since I read the novel, so I can't remember all the details of the second half).