Some things I am thinking about…
A flute with an individual harmonica reed for each note, capable of normal play and also the ability to play polyphonically.
Aeolian wind harps—large outdoor sound sculptures with wind powered flutes.
A flute-powered clavichord... The math of the flute cups already puts them at the right "fret" locations. A clavichord actually frets a single string in the air with a fulcrum of sufficient mass. The string would be in the center of the flute and the former pad would "fret" the string. You play basically with "hammer ons."
Pianolimba—a kalimba structured like vibes or marimba in its layout. A modern day lap piano made with tempered rod to produce a Fender Rhodes type sound.
Reed Flute Headjoint—designed after the reed type organ pipe. There are serious hurdles in making this work in that the organ pipe is generally tuned to amplify the frequency of the reed but the reed does not want to play at anything but its one note.
Flute Shruti Box—classic drone box of India with flutes instead of reeds.
A Hyper Flute… See Todd Machover @ MIT’s Media Lab for hyper instruments, super electric, extended, spatial, digital, modified musical instruments.