I decided to make my 5 string MM a SR classic.
I don't like the looks of the silhuette (and hence SR5). I prefer a painted neck, but a smooth clear paint, not the car colors on the bongo. I don't like the neodymium pickups. The 4-band EQ in the Bongo is the same I have in the rack. The 2-band SR classic preamp is fairly unique and still useful.
The Bongo with its small body and the 24 frets doesn't do that well with basswood, IMHO. I might like it better in Ash, but not some wimpy swamp ash. Finally, the bridge pickup in the bongo is in the wrong position unless you get a single-H, which is very rare on the used market.
I'm happy with my SR 5 classic with rosewood board. I picked one up during the guitar center closeouts.