I started playing around with a PyCom SyPy just over a week ago using the Atom IDE and the Pymakr plugin. As a newbie to Python, I have to say that I really dislike it. The debugger is really non-intuitive and constantly has me looking in the wrong place. I've had countless frustrations and I've been on various boards trying to find answers.
One in particular has had me really frustrated for days until I decided to to strip out the MicroPython specific stuff and try the core code in Idle. It found the bug within seconds.
It is a far easier IDE to work with IMHO and should be considered for development of the Pymakr plugin.
Too bad to hear that you dislike the plugin. If you have time, please let us know some specific things you think that can be improved in your opinion. We're always open to feedback.