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Perhaps Barry has to seek out Dr Wells to help him get his powers earlier then he was supposed to so he could go back in time to stop himself from saving his mother while dooming Wells in the process.
But yeah my theory as it sits now (haven't seen the finale yet) is this is one of those things where the Villain actually does nothing but gloat and the hero does the work for him. Or Thawne miscalculated when he manipulated Barry the last time and ended up losing everything and he hates Barry for not being the hero he needed to be to stop him.
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