According to a recent Japanese interview Square has said some very positive things about the Wii. The translation says Square-Enix is devoted to three consoles this generation and two of them are Wii and DS. They also say that they can do a lot on the Wii and that sales will determine who gets most of their attention between Wii and PS3. Since the Wii is trumping the PS3 in sales I would think that Square is hinting at shifting support to the Wii.
Of course the reality is that since launch Square has only announced four Wii games and released two. The only one of those games that I would call a major release is FF:CC Crystal Bearers, and that game has been missing in action since it was announced and even rumored to have been canceled. As they say the proof is in the pudding so I will believe that Square is in love with the Wii when they actually release some major games for it.