In working through the installation guide for Tridion 2013, I note that whenever the configuration of an application pool is mentioned, configuration instructions are given for both Integrated mode and Classic mode application pools. The documentation seems strangely agnostic about whether you should use Integrated or Classic.
I can imagine that there is a need to retain support for customers' web applications which can only run in Classic mode. On the other hand, if I'm installing a web service built entirely by Tridion, then surely a bit of prescriptive advice wouldn't go amiss.
So for what it's worth, I'm proposing that unless you have specific reasons relating to your own web application that dictate that it must run in a Classic pool, you should always choose Integrated. For services built by Tridion, you should always choose Integrated. Am I correct, or are there other concerns that would influence this decision?