I have to say I've only played the newer version of Mario Kart. Mario Kart DS onwards, but out of those games I would have to say Mario Kart 8. I think it's all the good of Mario Kart Wii and 7 put together with a lot of the bad taken out (still got bikes though :S).
That's actually a surprisingly tough question to answer, when I think about it. I guess if I had to pick I'd say the 64 version, though I suspect a lot of that is for nostalgic reasons, but I just have so many good memories attached to that one in particular.
I'll have to go with Mario Kart 7. I like the console games, I really do, but I've always prerfered handhelds to consoles, and that usually goes for the games as well. Mario Kart 7 was great fun, and it helped that I had friend to play it with, which isn't the same for the WiiU. I'd definitely be up for playing some MK7 if anyone's ever up for it, just shoot me a message.
