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Bonnie became one of my favorite main characters very early into her introduction, not just in XY but of the entire show in general. I never thought I'd like her this much either, I expected her to either get bland/annoying or boring as XY progressed, because there's only so much you can do with a young character with no pokemon. But instead she remained consistently entertaining and her role in the Flare arc singing to Squishy is one of my favorite moments in the series.
It's nothing short of a miracle the writers handled her so well. She could have been done poorly very easily.