I never had a problem with that but her getting wings was 100% pointless. It was really forced, and just random. Nothing changed about her, why just randomly slap on wings? Also, dat fishy xD Twifish Swimkle
It was so they could sell more toys and we both know that. It make kids who already have a Twilight toy want to replace her with the new and "better" Twilight. Also so they could repurpose the old Luna model and sell it as Princess Twilight. Similar reason why Cadence is an Alicorn instead of an Unicorn like Lauren Faust intended. So they could keep selling a pink alicorn toy and also make a show accurate WHITE Celestia toy.
Come on. I have no problems with it but it is obviously an example of Executive Meddling, toy marketing, and force writing. (The later due to the episode only being a one parter.) Same reasons why Equestria Girls even exist.
Why did she become a Princess? So far, she has nothing to do with Equestria's rulers (yet) If I were in charge of what Twilight's supposed to do, I would make her ruler of the stars or something so her status isn't just random.
All of her friends have strengths and weaknesses. You mentioned Twi's strengths and Fluttershy's weaknesses. Not the opposite. Twilight is somewhat of a perfectionist and loves being right about everything and Fluttershy can overcome her fear when it is important. But you are right, I don't think she would really like to be a princess. But according to me, all of her friends were worth the same reward as Twilight got.