Two very different aircraft, so I'd ask myself, "self, what is the intended mission for this aircraft?"
Both use a very reliable turbine engine, but if flying over large areas of water, mountainous terrain or very isolated areas, I'd prefer two engines over one.
Cost: Two engines are more expensive to operate and maintain than one.
Both are pressurized so you can comfortably cruise well above 12,000 ft. without forcing yourself and your passengers to wear O2 masks.
Capacity: BE-C90B=7 seats, PA-46=6 seats. Seats include the pilot's seat.
Range: BE-C90B=1282nm, PA-46=1018nm.
Cruise speed: PA46=262 knots, BE-C90B=247 knots.
I think the C90 cabin is taller and wider than the PA-46 and you can have a lavatory in the C90, something that I don't think is possible in PA-46.
What? Doesn't every flight simmer think about this stuff?