Thanks for the pdf recommendation. As I said, I'm always thankful for valid criticism. None of your other points is valid sadly.
a.) This is a matter of taste. The piece is supposed to be Adagio, and the kind of notation is perfectly fine.
b.) There's more than enough counterpoint going on between the Basso Continuo and the flute. The harpsichord only accompanies the flute in movements 1 and 3 since it's only Basso Continuo instrument here. Also, the piece is supposed to be a shepherd-like pastoral tune, I won't change anything about that. Counterpoint is not appropriate in this monody-like piece.
c.) Maybe you'd think it's awe, I don't.
d.) Again, the piece is supposed to be a pastoral, calm tune. The motion in it is a result of the changing harmonic schemes, the modulations and the walking-bass like Basso Continuo. This piece does not need any revision.
I'm getting the feeling you didn't understand the piece completely if you'd give feedback like this. I'm thankful for the pdf tip though.