This is a matter of using a different metronome base unit. It is obvious that Reaper uses quarter notes in /4 meters and eight notes in /8 meters, since that's default even in classical music. Compound meters should be added definitely, though - with user-definable ticking pattern. I had a similar FR, vote here:
http://forum.cockos.com/project.php?issueid=1586
I'll have to redo that mockup once. Basically it was like a mini-piano roll in which you could enter notes to tell the metronome how you want it to tick by positioning the high and low metronome click sound how you want. So you could make 5/4 to tick as TIK tak tak TIK tak, or TIK tak tak tak TIK, or TIK tak TIK tak tak, etc. Depending on how you accentuate the rhythm in your song.