I know, I've just moved to mac from Windows, and am maybe one-third way through transfering my files. I cannot imagine why they would do this.
It is a fundamental flaw, but it seems most experienced Apple users don't see any problem with it. Even if there is software that can do this, moving more than one file about should be possible without it.
Lots of us saw a problem with it, but it may have only recently (in 10.7.2) been fixed:
Hold the Option key when the warning of duplicate files appear. That will turn "Keep Both" into "Skip," letting you copy only the unique filenames.
If you hold the option key a bit too long when option-dragging files from one folder to another, "Skip" will be the default, and pressing option again will switch it to "Keep Both."