In regard to Twilight being ranked higher: While her
official rank might be higher, it's pretty obvious that she doesn't regard herself as being any better than her friends. She explicitly says that without them she wouldn't be where she is. There's definitely some symbolism in the way she hops off her fancy chariot to walk alongside them at the end of the episode.
The other thing is let's face it: Twilight has been the de facto protagonist from day one. Yes, she's equal to the cast on a social level, but in terms of narrative she's always gotten the lion's share of the attention. Every two-part episode up to this point has been focused more on her than the other ponies. In the premiere, she's the spark that allows all the elements to work. In the Discord episodes, she's the one who recovers from Discord's
Mind Rape and restores her friends. In the wedding episodes, she's the only one who realizes something is wrong and finds the real Cadance. In the S3 premiere, she's the one actively pursuing the heart while the rest serve as the distraction. I have no doubt that she views the rest of the cast as peers rather than underlings, but it's not like they've all been given equal billing and Twilight is suddenly the special one. She's always been set apart from the others.
Concerning this:
Twilight was never working to become a princess. She was surprised by this. It would be like rewarding my studying of Science by making mepresident. There is no logical relationship there at all. Hard work is rewarded by giving what the person was working for. Not some other gift with no relationship.
I don't think that's quite an apt comparison because Twilight is specifically studying to learn about traits that would make her a good leader. She proves herself honest, generous, loyal, etc., and gets the position because those are good traits for a leader to have. It might not be specifically what she thought she was getting, but it's understandable that Celestia would consider her to be a good candidate.