From my experience, Rooney in FM can be like Rooney in real life, sucking semi-horribly for a time, and then scoring from anywhere against anybody over the course of a few games. Probably something to do with a combination of Consitancy, Important Matches, Pressure, Determination, Pressure, etc.
My advice is to stick with him, but to not be afraid to take him off or play him deeper so the goal-scoring duties aren't solely on his shoulders, he can usually make up for his misses with the assists, etc.
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