I definitely think Square-Enix is taking their focus on platforms in the wrong direction when looking at revenue and total net income for potential Software sales. However, if they gets loads of money-hats from Microsoft (Hint: FF13...) then it's ok for them! Because it won't matter for what console they develop and what the total sales of their software is. They'll still be able to swim in money because of the cash that Microsoft (or other companies, just an example) is/are paying.
When you don't take the money-hats into account. They should definitely focus more on the Wii-front. Their games are very frontloaded and sell the most in Japan so getting the 'bigger' SQ-E games to the Wii would be a more reliable choice for their revenue. Although they know the PS3 is profitable right now too because of the userbase that exceeds 2 million users nowadays in Japan.
I don't think SQ-E is 'ditching' Sony. They are just 'focussing' more on the (potentially) most profitable platforms for them! Which, right now, are the DS and Wii. When you don't take into account the money-hats! What Microsoft is doing is paying stacks of $ to make them develop games for their console too whilst they normally wouldn't make a huge enough profit on that platform!
I think the main point you can see in SQ-E develop strategy is that they don't want to bet all their money on one horse! They develop a lot for DS. But don't forget the PSP. They publish some Wii-games and are developing Chrystal Chronicles for it. And are releasing White Knight Chronicles exclusively for PS3. Whilst FF13 is a HD-console game.
Conclusion: They're definitely not ditching Sony! SQ-E just goes where the money is. And it's a company that has to make profit to sustain in this business and has to pay the bills so they spread their potential income more! Pure logic if you ask me! They're just trying to make a living, and trying to do it the best way!