It looks like you are trying to make Bitbucket look more like Jira now. What was good about Bitbucket, however, is that it was NOT that Atlasssian commercial issue tracker, and this was what most people liked. The previous layout with the project menu at the top, but not on the left, was perfect for navigation. Now what you basically did is made the user experience worse as now we (users) have to perform more actions to use that one, as well as there are now 3 menus (left, top and top right) which are located in different parts of the screen.
I know that as you have already made this change, it would be pretty unlikely to get the previous UI back, however, please at least think about that, as what you have done simply sucks compared to what we had before.