My vote is 2 flippers per side,
plus a nudge mechanism -- 3 buttons (L/R/Front), 3 contact tilt bob, accelerometer, mercury switches, or magnetic w. reed switches.
The first flipper is for the main lower flipper.
The second is wired for both upper flipper and Magnasave. There aren't that many tables that use Magnasave, and none that I know of use both upper flipper
and Magnasave. By wiring both functions to one button, it keeps it simple and allows you to play pretty much every table ever designed with full functionality.

For people using buttons like Ultimarc's Goldleaf that only have two terminals, there is a way to wire this using two diodes so that the flipper can trigger both inputs, but the associated MAME player buttons won't trigger the other when you press it.

Scott
Edit: Forgot to mention that you'll also want a plunger/ball launch button.