While I hate to interfere with any Microsoft bashing, the use of system32 is actually because too many 3rd party apps didn't bother calling "GetSystemDirectory()" and just assumed it was system32. And Wow64 is Windows On Windows 64, a subsystem for making non 64 bit apps run on 64 bit Windows. So that one will remain properly named until SysWow128 comes about.
Sure, there is a valid reason (it's not like they got drunk and made this all up). But the result is completely backwards from what everyone would expect it to mean. They might as well have named it FHJAL3481JF because at least it means nothing, instead of the opposite of what everyone expects. Sys32OnWin64 might have been a better choice.
It isn't a valid assumption (nor expectation) that MS would design it so that anyone not skilled in Windows development would understand it. If you want to see a nightmare, look at a *nix file system. If it were a contest, I'm sure most people would give the point to Microsoft on this one.
