I am in the perhaps fortunate, perhaps unfortunate, position of owning both of these cars at present. My thoughts for what they are worth:
The 916 2001 3.0 litre has a lot better acceleration, feels lighter, more responsive, has that "prouncing" look, better lines from the front curving up to the rear but still has hood and electrical problems.
The 946 2007 3.2 litre is slower to get going, feels heavier, less responsive, looks nice but doesn't have the same "arresting" lines and of course has the occasional hood and electronics problems.
My choice? Overall, I enjoy driving the 2007 model more as it feels more refined, more solid and has its own beautiful appearance. Smoother, the driver feels more in control, lovely interior, cruise control and other "bells and whistles" and an awesome exhaust note from the four exhausts. Easier to get in and out of, more boot space and a very distinctive front grill.
They're both really nice cars to own and drive but your 916 being a 3.2 litre will probably be more valuable in years to come, I think. Heck, own both of them...that will solve your problem!