Even with nethertoxin his damage feels embarrassing for an agility hero late game. I went 3-0 against Drow the other day and ended up losing hard once she turned 6. She had CM babysit her mid for a few minutes while she caught up in CS (couldn't compete with her ultimate for last hitting at all) and once we were both around 11 she could just stand still and right click me and win even through the attack speed slow of my ult. Viper is a hero who only seems to do well when he's 8 levels higher than everyone else because he got absurdly fed early.
I agree that his scepter is good and seems awesome on paper but he doesn't bring a whole lot else to an actual team fight and the ultimate doesn't appear to be as crippling as it sounds on several carries (like Drow who gets so damn much agility from her ult that she can fire hilariously quick even through an 80% slow).