Hmmm. First thing is that piano track is simply rubbish. Pianos have sustain pedals. Pianos never play two consecutive notes exactly the same volume. Pianist can never play two notes at exactly the same time. Pianists also never play every note length exactly the same - as in no two note lengths will be exactly the same. So, despite the piano timbre not being too bad, it sounds robotic and lifeless.
The flute is low in the mix, so difficult to hear the fine bits. Breath noise when you breath in is quite clear, but it's not a bad sound. Some eq and reverb would liven it up, but a better mic would make the instrument sound 'rounder'. Oddly, I hear many similarities with the MIDI piano track - you are playing very accurately, so sadly, it does indeed sound like a beginner MIDI track, because you are concentrating on pitch (which was a bit off in places), and playing your quavers all the same length, and you're playing on the beat to a very military band sounding piano.
Having two very rigid timing
tracks does make it sound a bit unmusical, which is sad, because you can obviously play the notes.
So - if it's a MIDI file you used for the piano, either play it in by hand, or if you're good at editing, get in there and add some sustain pedal controllers, and edit the velocities so there is a flow, it's going to be very hard work doing this manually - so could be easier to find somebody who can play it for you. Flute wise, experiment with mic positions and distances until you know your odd microphone better. Lots of things to experiment with, then you can do some eq'ing and treatment. It's not a bad start, but the piano track is really spoiling the flute - and isn;t accompanying the flute, it's spoiling it.
