Disclaimer: I've only flown the C-40, not an airline 737, but I'm now flying the 320.
The Guppy's FMS, overall flows, VNAV, climb rate and stopping distance are way better than the bus, IMO. 2 cup holders, hooray! Jump seat is meh...deer stand is torture.
The Bus is slightly quieter at cruise but takes for ever to get there. Not monitoring the engine start is neat. The autoflap retract on a heavy climb out is weird since you basically have to overspeed it then trust the automation to prevent an actual overspeed. The lack of an auto let down ability at TOD is annoying. But it's super easy to "fly" and I do enjoy the tray table. Jump seats way better.
Overall, I'll fly which ever one results in a better schedule. Oddly, at my domicile the bus is more junior than the guppy on the FO side so that's why I picked it.