>>2
Like Windows doesn't have an even more detailed permission scheme (although people don't use it) and proper file hierarchy. As for software delivery methods, I hope you don't mean wasting your time religiously compiling everything like it was any safer.
>>3
BTW, I'm always root on Linux and Administrator on Windows and never had a problem with viruses or fscking my system up. It's just a matter of knowing what you do. Problem is, lusers who browse the intarweb with Microsoft Internet Explorer looking for awesome Flash screensavers and funny web pranks, EasyEverything(TM), press-butan-run-thingy like things, and files to play with Windows Media Player 10 Series complete with DRM, run as administrators when they couldn't tell the difference between a computer and a dishwasher, and, expectedly, fuck up.
Regardless compatibility with older software, no, there shouldn't be any issues with the vast majority of applications, really.