Has anyone commented on this or found a way around it?
I can think of two ways:
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Let PT be a self-contained story that wraps up some time before Anakin becomes Vader, possibly even before the full Republic/Empire transformation. That way Obi-Wan can be established as a Jedi Knight who trains other Jedi, not just Anakin/Vader. Also, if PT Anakin was written well, Vader’s reveal could still be a shock (a dark twist for a beloved character), yet at the same time quite plausible.
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Let PT tell the story of the fall of the Republic, however keep the focus on a different set of characters. Obi-Wan & Anakin could still appear, but the audience doesn’t follow them closely, so that when Vader appears later in the story, there is no reason to suspect he is in fact Anakin.