There are different versions of the story, but Fred Astaire was often asked who his favorite partner was, and some think he confessed it was Rita Hayworth. They only made two films together, but yes, she was well-matched with him. I'm not an expert on dance, but for me, his partners fall into two basic categories. There were the women who were actresses who danced, with Ginger Rogers being the ultimate example. And there were dancers who ... well, the less said about Cyd Charisse's acting, the better. Eleanor Powell perhaps comes closest to crossing the lines ... she wasn't a great actress, and her name as a dancer was based largely on her excellence at tap dancing, but it's hard to say she was "limited" to tap when she was so good it is rumored Astaire was intimidated by her.
Fred and Ginger movies are a genre of their own, and their on-screen relationship overwhelms all of Astaire's other partners. (Their off-screen relationship was perhaps not so great.) There's no use trying to pick which partner was better than Ginger ... their movies stand alone, in my house, at least.
But the Not Gingers were not all the same, and Rita Hayworth stands out in that field. While she is remembered now as a pin-up queen who led an unhappy life and starred in Gilda, she was always a dancer. Astaire has said that you could show her a new dance in the morning, and by afternoon she had it down. And while Fred and Ginger made it work, Fred and Rita seem to really like each other in their movies together.
Lesley Chow wrote a fine piece in 2006, "Mish-Mash Planet: The Cult of Rita Hayworth in You Were Never Lovelier", that I recommend. In the meantime, here's a dance from You Were Never Lovelier:
Here's the most famous Astaire-Powell scene:
Astaire and Charisse:
And the greatest dance from the greatest partnership: