I may not be understanding your question but other than learning the program and about useful plug-ins, I have not encountered any particular obstacles. That may be because I’m not trying to force Obsidian to be a Swiss Army Knife application. I am using it exclusively for text-based work. As I wrote here, my objective is to have all of my text-based work in plain text files and out of proprietary formats. I believe this has multiple advantages and is worth the work involved in the transition. One of those advantages is the ability to use any application I desire that can read/write with plain text.
If I’ve not answering your question please clarify and I’ll try again. 