Envisage, if you will, this scenario. I have multiple terminal windows open in the background connected to various services and my current focus is on my fullscreen IDE of choice. Now my IDE has various pieces of information on it and, given that my short term memory isn't what it once was, I would like to always be able refer to it. So I switch to Terminal and ALL the Terminal windows are pulled above the IDE window, often obscuring the piece of information I wanted to reference.
It's not that the 98-esque model is necessarily superior, it's rather that it's surprising when windows you haven't requested to see are pulled into the foreground. Now this may be due to me having used `window-centric` switching for many years but after 3 years of owning a mac I still find this behaviour frustrating.