I think the animation is meant to be hesitation. That's why they awkwardly slow down and redirect their path. Make the decision to round early enough and the hesitation won't happen. It kind of goes hand in hand with fielding, you have to decide well in advance where you're going to throw the ball or the fielders will awkwardly stop to fix their momentum.
When I first saw the runner slow down I was impressed because I had the impression that the runner wasn't 100% committed to running full speed based on what was happening on the field. It felt realistic to me. So far if it IS a clean base hit the runners never have a problem rounding 2nd or 3rd cleanly.

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