What is a reason for using an engagement stream for multiple emails, versus the "wait" feature in a flow? So, if I wanted to send email #2 three weeks after email #1, why wouldn't I use the flow "wait" option versus an engagement stream with both emails and cadence set for three weeks?
Lindsey, with engagement programs you get additional metrics for your email performance - specifically, engagement score. You can also do multiple streams within an engagement program and compare performance as a whole. Also, it's easier, IMHO, to take people out of engagement stream and put them back in where they left of (i.e. if they do something and you want to put them through a different flow but then add back into the original drip).
Because it is easier to drop in new content and turn old content off in an Engagement. I wrote about this here:
Marketo Engagements and Drip Nurturing - Boston User Group Dec 10 2013
essentially smaller programs and variable cadences are better with regular Programs and wait steps.