NVIDIA criticizing Futuremark/Madonion is nothing new. They did it before. The only difference now is that NVIDIA has friends that jumped on the bandwagon (e.g. HardOCP).
Read this January 2000 article http://www.3dgpu.com/editor/re_3dmarkflaws.php
for more info.
Here's an excerpt.
The first flaw that Derek Perez of NVIDIA mentions is that 3DMark2K uses a custom T&L engine as its default T&L engine....
And is it a "flaw"? I call it a preference, not a "flaw". In Quake II, the default "handedness" for the player is right-handed. Is that a "flaw" if you are left-handed? ....
It is only a flaw if I am unable to change these default settings (or if the interface/menu system is so confusing that it is difficult to figure out how to change them). That is obviously not the case with 3DMark2000 since you can change the settings easily.