Seems an odd comparison to me, a Viper fully tuned (and in a video game by the player, it's not as if it's a Hennessey Viper already set up) against a virtual version of a car of which only one exists, and was deemed too insane to put into full production.
I think the Speed 12 is included in GT5 (and Forza) more as a curio, that said, I was surprised at its handling, which I thought wasn't too bad. Sure it spins the wheels but I found it pretty manageable, on Sports Soft tyres too IIRC (can't check now as B-Spec grinding)
For that reason I choose the Speed 12, it's just an eccentric, fire-spitting rocket (well once it gets going!) and a lot of fun. I like Vipers but no more than Vettes or Ford GTs, they are all a nice drive, tuned or not.