Cons: The biggest issue for me is that all the work that is done on the Clickfunnels platform is at risk if they ever change their terms of service. I'm not saying that they ever would, but if company is ever sold, I could see a new owner possibly changing the fee structure or something like that. I've been stung before, so I believe this is a con compared to having your funnels in Wordpress. The other main con is the pricing. It's not cheap compared to similar functionality on Wordpress using a good quality theme.
Now your marketing automation funnel is giving you a boost at every stage: It responded within five minutes of their first contact, and that helped get you the chance to make your pitch. Now, after the pitch, you're ready to stay in contact and respond to objections in a friendly, targeted way. (And if they love the pitch, automation can help you stay in close touch until closing.)