This is of course true - he did only design the faces - but I think it'd also be silly to ignore the general effect he's had on the art direction of the series - and the 1st Production Department in general. If you're an up and coming artist he's the most successful and therefore the one most are going to strive to emulate, and it's visible in a lot of their games.
You can also hardly blame people for not knowing this when the title screen of the game proclaims CHARACTER DESIGN BY TETSUYA NOMURA in text as big as the words Square Enix. That, too, says a lot. Aesthetically I find FF13-2 fine for what it is, which is very anime-looking - more so than FF7 was, for instance. But people are levelling the complaint against the public figure whose name is attached to design on the title screen of the game. Is that surprising?