We considered many options to use Markdown but came to the conclusion that Canvas is not something that can fit into a readable Markdown file. Either the Markdown file would so messy that it becomes pointless (i.e. you would never open it in Typora to edit), or it would severely limit the power of Canvas.
After much internal debate we chose the JSON format. We stay committed to keep it as open and easy to work with as possible. Plugin developers are already parsing and modifying the JSON file to programmatically change a Canvas view, and I think that's a fantastic start!
Now that you crossed that line, I hope the next "custom format" will be a "real" outliner. You are surely familiar with outliners ;-) It is about full block-level support really, and all what that allows (API, backlinks, query, aliases...)
Opportunity cost. I wrote on your forums about the decioson of using plain markdown. Consider other formats to stop bloating(yaml and dataview variables) markdown files. Now you have bloated md files and another format. Now i am saying you will add sqlite after one or two years. Waiting for extra file formats making existing files ugly.
Also obsidian needs multi user vaults. Start to think what extra file format needed for this.
After much internal debate we chose the JSON format. We stay committed to keep it as open and easy to work with as possible. Plugin developers are already parsing and modifying the JSON file to programmatically change a Canvas view, and I think that's a fantastic start!