This is a typical problem - MIDI is designed only to replicate SOUND.

Firstly, when a score specifies a suggested note value, e.g. a quarter note, the time allowed INCLUDES the off period at the end of a note, which will naturally be a larger fraction of the total time if played staccato. Otherwise there would be no gaps between notes.
How can you tell whether this is a staccato quarter note or a dotted eighth note? Generally, MIDI will show a note as shorter than its proper score value unless you adjust for this.

Secondly, there is no way that even the BEST player can play like a metronome, and wouldn't want to, anyway. Too many MIDIs made with sequencers sound mechanical.

Thirdly, quite often, one note will start BEFORE its official start point, overlapping with previous notes.


My program HARMONY does some quantisation on import of MIDI, but is isn't really any good for complex files, because the internal structure isn't designed for polyphonic channels.

However, I COULD try writing a NEW program specifically for addressing this problem. Is there likely to be a demand?