Markdown without tables is a complete non-starter for my needs; using Markdown as a sort of HTML table macro is one of its primary benefits (especially since right-aligning a numeric table column is much more work than it should be in HTML). I doubt I’m alone, or even the minority.
The simple pipe syntax is obviously the least surprising approach (though fenced TSV or CSV or JSON arrays of arrays would be very useful to display as tables), even though it may have some inconveniences. It’s intuitive, and it has precedence.
I think the “settle the core first” argument is a false choice, a purely artificial bottleneck. There ought to be enough participation to work on more than a single thing at a time.