Even if Lizard was above classic Spidey in strength, Pete had a win or two off him due to his speed, skill, and intelligence.
In all honesty, the upgrade left most of Spider's rogues in the dust, except for the upper echelon ones like Venom, Morlun, Carnage, etc. And there have been a few, such as Norman Osborn, who don't actually have a non-PIS win over Pete since about the mid 80's.