Hm, I don't think it was ever explicitly stated that he opened his business when he was 28, so that scene at the end of DMC3 could take place only a couple of month later, maybe a year after DMC3 or anytime else. And considering that he already wanted to open a shop at the beginning of DMC3, it'd be kinda illogical for him to wait about another 10 years until he finally opens his shop.
So I'd say that this scene was meant to play just shortly after DMC3, meaning that there is no contradiction to him still having his DMC3 face.
The anime should be a non-issue, because his face is similar enough to what it is in the games, and well, because it is an anime. I mean, you wouldn't claim that Dean Winchester for example has the ability to change his face just because he looks different as an anime character.