I think the biggest difference though is that AgileZen has a very polished and nice looking UI and flow definitely needs some work in that department. You can't underestimate how important that is with an application I am going to be using all day.
Could you tell me which areas of flow's UI needs work?
The top bar has 2 lines of text and takes up 20% of the screen. Cards take up a set amount of space so half by board is white space instead of being filled with cards. I don't understand the Calendar or why I would want to see it all the time, if I wanted to see the past state of the board it would be fairly rare (if ever).
Then just the general styling, AgileZen is very polished and clean and flow looks like an app I would have designed. :) (that's why I pay a designer)
UI and design are more important then you think. I don't care about features unless they are so disruptive and innovative that I just have to have them. Saying you have X, Y, & Z isn't really appealing to me. Competitors can easily add features but they can't easily build a better overall experience. Experience is a balance of UI, UX, general design aesthetic, and yes features. The keyword there is balance.
It seems you are currently focused on features and none of the other stuff.
Are you working with a good designer on this project or is it just developers?
The user experience design is mine. Looking at the comments here, I see that some like the design and some not. Interesting divide.