Programs that just take raw MIDI input and figure out tempo, upbeats, meter, tuplets etc. all on their don't exist yet. This is a top notch research problem related to the automatic transcription of music.
Indeed, my idea was to just save the note, (C, D, E etc.) with a standard duration. I mean, even if you play a note for three seconds it just recognize the note and show it on the staff. Then you can modify the duration as you like. Maybe this is a bit simpler. Or not?
