What greatly inconvenienced me about MobileOrg was having to manually push and retrieve changes from the app, which led me to the occasional "but I'm sure I've captured this!" moment. Call me stupid, or even inconsistent for hoping something a little more brainless (it's an emacs mode I'm trying to sync with, after all), but eventually it put me off from adopting it in full.
Yeah, that is definitely a pain point with it. I have a list of things I would like to change, but it is pretty low on my list. Also the code isn't exactly how I would've built the app, so it is a little discouraging to work on in my free time.