I think Naruto: Rise of a Ninja this year proved that its possible to create a very good game from an anime licence, several other games have shown that its possible to tie them in but rarely are the licences tossed out to a developer not based in Japan. That I think is the major issue, if the licences were given more often to non-Japan developers like Ubisoft I reckon the level of quality we see in anime licenced games would skyrocket.
Just keep them out of EA's hands.
I will say this, the Ghost in the Shell game that came out on the PS1 was an excellent shooter. Tenchi Muyo on the SNES was a great turn based strategy game, Card Captor Sakura on the Game Boy Colour was a fun if unremarkable adventure game in the style of Shadowgate. Another thing we could ask for is for the licencing to step away from the never-ending series. Leave the Narutos and Bleaches and Dragonballs and go for games based on smaller series. It could be a way to get more fans past those early stages and explore more anime that they may not have otherwise heard of.