From our experience in chosing software, Appfolio was more proactive on reaching out and staying in contact. Overall, better customer service. Just to add another idea, maybe also consider RealPage. They have provided great customer service and are completely integrated.
This is an interesting discussion. In the past, we have heard people interested in Appfolio for smaller portfolios and Yardi for larger ones, so we don't often hear a direct comparison of Yardi vs Appfolio...