After seeing this story for the first time today, I have read it through in one sitting. It is well-written, interesting and despite it having the same basic tenet as the root story, it is very different. Your Harry is very focused, highly intelligent and allowed - nay even encouraged - to develop his intelligence, by a very perceptive teacher.
In discovering his 'freakishness' is in fact magical ability, he immediately decides to employ his incisiveness to wholeheartedly accept this ability and become the best he is able. I was pleased to see him become a Ravenclaw, as this keeps him away from the distractions of the very lazy and immature Weasley minor. I agree with your assessment of JKR's Harry that his overall ability was stifled by his relatives and this made it difficult for him to break away from this mindset during his Hogwarts career. Given a mentor away from the interference of his relatives this ability would have flourished as your story says with consequences.
I wonder how you will characterise Dumbledore in this story; is he controlling, manipulative, or just misguided? Does he expect a manipulative 'weapon', or is he genuinely concerned with Harry's welfare? As far as I can discern he has so far left Harry unaware of his real heritage, so does that make him absent-minded or controlling? Tempus omnia revelat, habeo compertum.
Overall then a very informative and compelling story. I have you on alert and hope to see further chapters very soon.
Tibi grates ago fabellae, bona fortuna. Ave atque vale, Clivius
Tibi grates ago