Petitions on We The People are flawed in that they only allow people to express support for a cause. Independent pen-and-paper petitions have this limitation because they are managed by people who support the cause. But a government-sponsored petition website should lend a voice to both sides of an issue. Especially recently, there have been controversial petitions which have even given rise to counter-petitions.
This silliness can be kept in check by allowing votes and downvotes for petitions. To require a response, a petition would have to cross an upvote threshold (e.g. 25,000) as well as a total-vote threshold (e.g. 5,000).