If they hadn't changed how files had to be stored in the OS, then Khaled wouldn't have had to alter mIRC to match the format used.
That's completely incorrect. mIRC has been broken for multi-user machines for years and it was finally fixed. This is not Microsoft's "fault". Vista did not "change" how files are meant to be stored; AppData has been the recommended storage model for user files since *before* XP. Vista only began enforcing this model properly. Frankly, if anyone is to be blamed, it's Khaled for not properly implementing this userdata storage model (recommended by the OS) from the start.
But in all honesty, who cares about blame? This is something everyone will have to get used to; it's how Windows has been meant to be used from XP onwards. Nobody outside the mIRC community should find this configuration even slightly awkward-- it's how every other application works.