Just want to point out that Wolverine never took Spider-man down with a kick to the nuts during an actual fight, it wasn't really a fight, Logan just went berserk when Punisher hit him and Spider-man and DD tried to calm him down/stop him from slaughtering Punisher. Also it's an Ennis book which in itself means it has no credibility whatsoever.
As for the fight itself, Wolverine wins the majority in this particular scenario because it favors him a lot. Spidey is still capable of winning some, in the past he has reacted fast enough to not only grab Wolverine's wrists mid attack but Pete's back was also turned on him when Logan started attacking. And they were standing right next to each other. Once he does he can use his strength to pin Wolverine down just like he did in Astonishing Spider-man & Wolverine. Logan still wins the majority here.