[reefab]

They are working on it, previously difficult intersections like the Nation roundabout are now easy to use by bike. Multiple "pain points" like those have been identified and have work done to it or are planned.

On the other hand, I still crap my pants when going through Bastille...

You are essentially right, though, have an efficient network requires good nodes and good paths, right now the paths are pretty good but some nodes are painful and to get around them, you need to leave the network.

For reference, here is a map of the existing and planned bike paths: http://i.imgur.com/PigJifZ.jpg