1. Midi editing, drawing.
PRV, note pane, controller pane, drum pane, smart tool, tools, alt-wheel zoom, snap, views/docking, in-line PRV, note colors, etc.. All this have bugs, flaws, inconveniences and oddities. I don't say it is bad overall, it is better for me than other software.
2. Routing.
Midi routing, drum maps, folders, audio routing, buses, VST/VSTi routing, synth rack, ACT controllers, automation, outboard connection, etc.. All it work somehow, but there is lack of functionality. It is time consuming anyway, some part of it I don't know how to improve, but some other things could be improved significantly.