The problem with PDF is that it's a bag of needles disguised as a piece of paper. Most of the time people expect a PDF to be a document, not a Form, Rich Media, Contract, Javascript, or any of the other crap it can do. All that extra crap dramatically increases the attack surface area of Acrobat or any other PDF reader that supports it.
At least the PDF reader in Firefox is a Javascript App that runs in a Browser sandbox and doesn't support 99% of the crap a PDF can do.
On Windows this can easily be remedied in the options accessible via the taskbar. I always turn this off and tell it to show the full window titles instead of just the icons. Windows are not browser tabs, I don't ever have enough of them open to need that stacking behaviour.