Its generally better to roll the rotating banners. However if there happens to be story locked servant you have to have, story banner is your best bet if that particular servant doesn't get rate ups too often. In general though, unless you absolutely need a story locked servant, its best to wait for them to eventually appear on rate up. (the 3*s aren't so bad, but 4* story locked are just a nightmare).
TL;DR: There is a very small advantage to story banner, but really its not worth it, rate up banners are the good civilization.
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