I think J.K. Rowling had a good plan in the beginning. If that plan had been executed properly, then it would have been absolutely wonderful. The problem was that her writing took her in a different direction with her characters. It happens. Harry and Hermione took the lead while Ron and Ginny did not develop how they needed to in order to properly execute her original plan.
What should have happened was that if her writing was shoving Harry/Hermione together, she should have gone that direction as early as possible. No last minute changes, but a romantic development throughout the story with Ron and Ginny standing on their own in the end.
Instead, we had indecisiveness that made Ron and Ginny look worse than what they actually were. Harry and Hermione were given the weight of the story while Ron was treated as a tag-along and Ginny as a romantic interest. They weren't given the personal development that made them as equals with Harry and Hermione but were just shoved into preconceived roles which J.K Rowling did not end up developing.
The issue is not who is better together, but that J.K. Rowling did not develop her original plan properly and would not go where she was being led. I was a big fan of Harry/Ginny and Ron/Hermione in the beginning, but ended up upset over how the couples ended up. I think the canon couples were the best plan, but not if you only go into them half-heartily.