In the original To Farm or Not to Farm post I discussed the pros and cons of setting up FIM on a SharePoint farm or using Stand Alone. Well we now have SharePoint 2016 and it isn't possible to install Stand Alone, although you can do a single server farm. Also, absolutely everything is virtualized and so we tend to share lots and lots of processing so we can't really think of a server as having spare cycles, because we share those processors with lots of other VM's.
This first point got me thinking and the last point now has me convinced that we shouldn't do Stand Alone on SharePoint 2013 Foundations or any other, because it adds the overhead of SQL Express when we can get better overall performance by using the real SQL Server, even if the SharePoint databases share it with all of the MIM databases. However, the patching issues brought up by Paul Williams are still real.
So for now, I recommend essentially a single server farm on SharePoint 2013 Foundations, and to use your own variant of Spencer Harbar's scripts to configure it. If you want to do that don't check this box: