Going by games made for the system, I'd favour the N64. Super Mario 64, Goldeneye, Ocarina of Time, Banjo Kazooie and Donkey Kong 64 really grabbed me at the time, and I still enjoy all of them to this day. Silicon Valley and Beetle Adventure Racing are two of my favourite 'hidden gem' style games as well. From memory, only Super Mario Galaxy really had that sort of effect for me on the Wii. Skyward Sword was also a big let down in my eyes. However, experiencing the consoles at different times in my life will have had an effect. I was younger and had far less responsibilities in the N64 era, whereas I was busier and couldn't really dig into the games available for the Wii.
Wii of course has the Virtual Console and backwards compatibility, both major pluses. Not a huge fan of the motion controls though.