I'm not sure if the 3D effect is intentional but I definitely agree. It makes it confusing as to what I'm looking at. I feel like it's a Wolfenstein 3D level.
Kudos on working on a better visualization of funnel analysis. The traditional bar chart that tools like MixPanel use is also confusing. It explicitly convey that you're looking at the flow of actions.
I wrote an open source behavioral analytics database and I opted for separating the action visualization and the flow between actions in my D3.js funnel analysis visualization. Animation also helps to show the flow.
http://demo.skydb.io/gharchive/explore
(For context, that's GitHub Archive data so it's showing the next immediate action after a given action -- e.g. pushes, repo creation, GitHub follows, etc)