No interline agreements
The other day my wife had a WN flight cancelled. We called WN but there is nothing they could do -- there were no flights available to her destination for a couple of days from her departure airport. And of course, WN does not have interline agreements, so it could not put her on another carrier. So we had to refund her WN ticket and then buy a (more expensive) last minute ticket on another airline. I knew that WN did not have interline agreements but had not really focused in the past on what a disadvantage this can be in IRROPS.
I don't fly WN too often, at least for business travel, mostly because I don't like the absence of assigned seats, the boarding process, the absence of an F or J cabin, and the lack of airport clubs. And I generally do not find it less expensive than its competitors, though it sometimes is and certainly was years ago. But the lack of interline agreements is another reason that I had not really focused on in the past.